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Zhang X, Zhang D, Zhang X, Zhang X. Artificial intelligence applications in the diagnosis and treatment of bacterial infections. Front Microbiol 2024; 15:1449844. [PMID: 39165576 PMCID: PMC11334354 DOI: 10.3389/fmicb.2024.1449844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 07/04/2024] [Indexed: 08/22/2024] Open
Abstract
The diagnosis and treatment of bacterial infections in the medical and public health field in the 21st century remain significantly challenging. Artificial Intelligence (AI) has emerged as a powerful new tool in diagnosing and treating bacterial infections. AI is rapidly revolutionizing epidemiological studies of infectious diseases, providing effective early warning, prevention, and control of outbreaks. Machine learning models provide a highly flexible way to simulate and predict the complex mechanisms of pathogen-host interactions, which is crucial for a comprehensive understanding of the nature of diseases. Machine learning-based pathogen identification technology and antimicrobial drug susceptibility testing break through the limitations of traditional methods, significantly shorten the time from sample collection to the determination of result, and greatly improve the speed and accuracy of laboratory testing. In addition, AI technology application in treating bacterial infections, particularly in the research and development of drugs and vaccines, and the application of innovative therapies such as bacteriophage, provides new strategies for improving therapy and curbing bacterial resistance. Although AI has a broad application prospect in diagnosing and treating bacterial infections, significant challenges remain in data quality and quantity, model interpretability, clinical integration, and patient privacy protection. To overcome these challenges and, realize widespread application in clinical practice, interdisciplinary cooperation, technology innovation, and policy support are essential components of the joint efforts required. In summary, with continuous advancements and in-depth application of AI technology, AI will enable doctors to more effectivelyaddress the challenge of bacterial infection, promoting the development of medical practice toward precision, efficiency, and personalization; optimizing the best nursing and treatment plans for patients; and providing strong support for public health safety.
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Affiliation(s)
- Xiaoyu Zhang
- First Department of Infectious Diseases, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Deng Zhang
- Department of Infectious Diseases, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Xifan Zhang
- First Department of Infectious Diseases, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xin Zhang
- First Department of Infectious Diseases, The First Affiliated Hospital of China Medical University, Shenyang, China
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2
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Ernst R, Renne MF, Jain A, von der Malsburg A. Endoplasmic Reticulum Membrane Homeostasis and the Unfolded Protein Response. Cold Spring Harb Perspect Biol 2024; 16:a041400. [PMID: 38253414 PMCID: PMC11293554 DOI: 10.1101/cshperspect.a041400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The endoplasmic reticulum (ER) is the key organelle for membrane biogenesis. Most lipids are synthesized in the ER, and most membrane proteins are first inserted into the ER membrane before they are transported to their target organelle. The composition and properties of the ER membrane must be carefully controlled to provide a suitable environment for the insertion and folding of membrane proteins. The unfolded protein response (UPR) is a powerful signaling pathway that balances protein and lipid production in the ER. Here, we summarize our current knowledge of how aberrant compositions of the ER membrane, referred to as lipid bilayer stress, trigger the UPR.
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Affiliation(s)
- Robert Ernst
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Mike F Renne
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Aamna Jain
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Alexander von der Malsburg
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
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3
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Xia H, Horn J, Piotrowska MJ, Sakowski K, Karch A, Kretzschmar M, Mikolajczyk R. Regional patient transfer patterns matter for the spread of hospital-acquired pathogens. Sci Rep 2024; 14:929. [PMID: 38195669 PMCID: PMC10776674 DOI: 10.1038/s41598-023-50873-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024] Open
Abstract
Pathogens typically responsible for hospital-acquired infections (HAIs) constitute a major threat to healthcare systems worldwide. They spread via hospital (or hospital-community) networks by readmissions or patient transfers. Therefore, knowledge of these networks is essential to develop and test strategies to mitigate and control the HAI spread. Until now, no methods for comparing healthcare networks across different systems were proposed. Based on healthcare insurance data from four German federal states (Bavaria, Lower Saxony, Saxony and Thuringia), we constructed hospital networks and compared them in a systematic approach regarding population, hospital characteristics, and patient transfer patterns. Direct patient transfers between hospitals had only a limited impact on HAI spread. Whereas, with low colonization clearance rates, readmissions to the same hospitals posed the biggest transmission risk of all inter-hospital transfers. We then generated hospital-community networks, in which patients either stay in communities or in hospitals. We found that network characteristics affect the final prevalence and the time to reach it. However, depending on the characteristics of the pathogen (colonization clearance rate and transmission rate or even the relationship between transmission rate in hospitals and in the community), the studied networks performed differently. The differences were not large, but justify further studies.
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Affiliation(s)
- Hanjue Xia
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical School of the Martin Luther University Halle-Wittenberg, 06108, Halle, Saale, Germany.
| | - Johannes Horn
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical School of the Martin Luther University Halle-Wittenberg, 06108, Halle, Saale, Germany
| | - Monika J Piotrowska
- Institute of Applied Mathematics and Mechanics, University of Warsaw, 02-097, Warsaw, Poland
| | - Konrad Sakowski
- Institute of Applied Mathematics and Mechanics, University of Warsaw, 02-097, Warsaw, Poland
| | - André Karch
- Institute for Epidemiology and Social Medicine, University of Münster, 48149, Münster, Germany
| | - Mirjam Kretzschmar
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands
| | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical School of the Martin Luther University Halle-Wittenberg, 06108, Halle, Saale, Germany
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4
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González-Gordon L, Porphyre T, Muwonge A, Nantima N, Ademun R, Ochwo S, Mwiine NF, Boden L, Muhanguzi D, Bronsvoort BMDC. Identifying target areas for risk-based surveillance and control of transboundary animal diseases: a seasonal analysis of slaughter and live-trade cattle movements in Uganda. Sci Rep 2023; 13:18619. [PMID: 37903814 PMCID: PMC10616094 DOI: 10.1038/s41598-023-44518-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/09/2023] [Indexed: 11/01/2023] Open
Abstract
Animal movements are a major driver for the spread of Transboundary Animal Diseases (TADs). These movements link populations that would otherwise be isolated and hence create opportunities for susceptible and infected individuals to meet. We used social network analysis to describe the seasonal network structure of cattle movements in Uganda and unravel critical network features that identify districts or sub-regions for targeted risk-based surveillance and intervention. We constructed weighted, directed networks based on 2019 between-district cattle movements using official livestock mobility data; the purpose of the movement ('slaughter' vs. 'live trade') was used to subset the network and capture the risks more reliably. Our results show that cattle trade can result in local and long-distance disease spread in Uganda. Seasonal variability appears to impact the structure of the network, with high heterogeneity of node and edge activity identified throughout the seasons. These observations mean that the structure of the live trade network can be exploited to target influential district hubs within the cattle corridor and peripheral areas in the south and west, which would result in rapid network fragmentation, reducing the contact structure-related trade risks. Similar exploitable features were observed for the slaughter network, where cattle traffic serves mainly slaughter hubs close to urban centres along the cattle corridor. Critically, analyses that target the complex livestock supply value chain offer a unique framework for understanding and quantifying risks for TADs such as Foot-and-Mouth disease in a land-locked country like Uganda. These findings can be used to inform the development of risk-based surveillance strategies and decision making on resource allocation. For instance, vaccine deployment, biosecurity enforcement and capacity building for stakeholders at the local community and across animal health services with the potential to limit the socio-economic impact of outbreaks, or indeed reduce their frequency.
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Affiliation(s)
- Lina González-Gordon
- The Epidemiology, Economics and Risk Assessment (EERA) Group, The Roslin Institute at The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
- Global Academy of Agriculture and Food Systems, Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Thibaud Porphyre
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, Universite Claude Bernard Lyon 1, CNRS, VetAgro Sup, Marcy l'Étoile, France
| | - Adrian Muwonge
- The Epidemiology, Economics and Risk Assessment (EERA) Group, The Roslin Institute at The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- The Digital One Health Laboratory, The Roslin Institute at The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Noelina Nantima
- Department of Animal Health, Ministry of Agriculture Animal Industry and Fisheries, Entebbe, Uganda
| | - Rose Ademun
- Department of Animal Health, Ministry of Agriculture Animal Industry and Fisheries, Entebbe, Uganda
| | - Sylvester Ochwo
- Center for Animal Health and Food Safety, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Norbert Frank Mwiine
- Department of Biomolecular Resources and Biolaboratory Sciences (BBS), College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Lisa Boden
- Global Academy of Agriculture and Food Systems, Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Dennis Muhanguzi
- Department of Biomolecular Resources and Biolaboratory Sciences (BBS), College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Barend Mark de C Bronsvoort
- The Epidemiology, Economics and Risk Assessment (EERA) Group, The Roslin Institute at The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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5
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Agosta M, Bencardino D, Argentieri M, Pansani L, Sisto A, Ciofi Degli Atti ML, D'Amore C, Bagolan P, Iacobelli BD, Magnani M, Raponi M, Perno CF, Andreoni F, Bernaschi P. Clonal Spread of Hospital-Acquired NDM-1-Producing Klebsiella pneumoniae and Escherichia coli in an Italian Neonatal Surgery Unit: A Retrospective Study. Antibiotics (Basel) 2023; 12:antibiotics12040642. [PMID: 37107005 PMCID: PMC10135170 DOI: 10.3390/antibiotics12040642] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
This article reports a rapid and unexpected spread of colonization cases of NDM-1 carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in a neonatal surgical unit (NSU) at Bambino Gesù Children's Hospital in Rome, Italy. Between the 16th of November 2020 and the 18th of January 2021, a total of 20 NDM-1 carbapenemase-producing K. pneumoniae (n = 8) and E. coli (n = 12) were isolated from 17 out of 230 stool samples collected from neonates admitted in the aforementioned ward and time period by an active surveillance culture program routinely in place to monitor the prevalence of colonization/infection with multidrug-resistant Gram-negative microorganisms. All strains were characterized by antimicrobial susceptibility testing, detection of resistance determinants, PCR-based replicon typing (PBRT) and multilocus-sequence typing (MLST). All isolates were highly resistant to most of the tested antibiotics, and molecular characterization revealed that all of them harbored the blaNDM-1 gene. Overall, IncA/C was the most common Inc group (n = 20/20), followed by IncFIA (n = 17/20), IncFIIK (n = 14/20) and IncFII (n = 11/20). MLST analysis was performed on all 20 carbapenemase-producing Enterobacterales (CPE) strains, revealing three different Sequence Types (STs) among E. coli isolates, with the prevalence of ST131 (n = 10/12; 83%). Additionally, among the 8 K. pneumoniae strains we found 2 STs with the prevalence of ST37 (n = 7/8; 87.5%). Although patient results were positive for CPE colonization during their hospital stay, infection control interventions prevented their dissemination in the ward and no cases of infection were recorded in the same time period.
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Affiliation(s)
- Marilena Agosta
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
| | - Daniela Bencardino
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61032 Fano, Italy
| | - Marta Argentieri
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
| | - Laura Pansani
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
| | - Annamaria Sisto
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
| | | | - Carmen D'Amore
- Clinical Pathways and Epidemiology Unit, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Pietro Bagolan
- Neonatal Surgery Unit, Medical and Surgical Department of the Fetus-Newborn-Infant, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Barbara Daniela Iacobelli
- Neonatal Surgery Unit, Medical and Surgical Department of the Fetus-Newborn-Infant, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61032 Fano, Italy
| | - Massimiliano Raponi
- Health Directorate, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
| | - Francesca Andreoni
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", 61032 Fano, Italy
- Clinical Pathology Unit, Azienda Sanitaria Territoriale, 61029 Urbino, Italy
| | - Paola Bernaschi
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, 00163 Rome, Italy
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6
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Wang C, Wang B, Pandey T, Long Y, Zhang J, Oh F, Sima J, Guo R, Liu Y, Zhang C, Mukherjee S, Bassik M, Lin W, Deng H, Vale G, McDonald JG, Shen K, Ma DK. A conserved megaprotein-based molecular bridge critical for lipid trafficking and cold resilience. Nat Commun 2022; 13:6805. [PMID: 36357390 PMCID: PMC9649747 DOI: 10.1038/s41467-022-34450-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/25/2022] [Indexed: 11/12/2022] Open
Abstract
Cells adapt to cold by increasing levels of unsaturated phospholipids and membrane fluidity through conserved homeostatic mechanisms. Here we report an exceptionally large and evolutionarily conserved protein LPD-3 in C. elegans that mediates lipid trafficking to confer cold resilience. We identify lpd-3 mutants in a mutagenesis screen for genetic suppressors of the lipid desaturase FAT-7. LPD-3 bridges the endoplasmic reticulum (ER) and plasma membranes (PM), forming a structurally predicted hydrophobic tunnel for lipid trafficking. lpd-3 mutants exhibit abnormal phospholipid distribution, diminished FAT-7 abundance, organismic vulnerability to cold, and are rescued by Lecithin comprising unsaturated phospholipids. Deficient lpd-3 homologues in Zebrafish and mammalian cells cause defects similar to those observed in C. elegans. As mutations in BLTP1, the human orthologue of lpd-3, cause Alkuraya-Kucinskas syndrome, LPD-3 family proteins may serve as evolutionarily conserved highway bridges critical for ER-associated non-vesicular lipid trafficking and resilience to cold stress in eukaryotic cells.
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Affiliation(s)
- Changnan Wang
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Bingying Wang
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Taruna Pandey
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jianxiu Zhang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Fiona Oh
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Sima
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Ruyin Guo
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, USA
| | - Yun Liu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chao Zhang
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaeri Mukherjee
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Michael Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Weichun Lin
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huichao Deng
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Goncalo Vale
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey G McDonald
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kang Shen
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Dengke K Ma
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
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7
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Agosta M, Bencardino D, Argentieri M, Pansani L, Sisto A, Ciofi Degli Atti ML, D’Amore C, Putignani L, Bagolan P, Iacobelli BD, Dotta A, Martini L, Di Chiara L, Magnani M, Perno CF, Andreoni F, Bernaschi P. Prevalence and Molecular Typing of Carbapenemase-Producing Enterobacterales among Newborn Patients in Italy. Antibiotics (Basel) 2022; 11:antibiotics11040431. [PMID: 35453183 PMCID: PMC9032973 DOI: 10.3390/antibiotics11040431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/10/2022] Open
Abstract
The spread of carbapenemase-producing Enterobacterales (CPE), especially Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli), is a serious public health threat in pediatric hospitals. The associated risk in newborns is due to their underdeveloped immune system and limited treatment options. The aim was to estimate the prevalence and circulation of CPE among the neonatal intensive units of a major pediatric hospital in Italy and to investigate their molecular features. A total of 124 CPE were isolated from rectal swabs of 99 newborn patients at Bambino Gesù Children’s Hospital between July 2016 and December 2019. All strains were characterized by antimicrobial susceptibility testing, detection of resistance genes, and PCR-based replicon typing (PBRT). One strain for each PBRT profile of K. pneumoniae or E. coli was characterized by multilocus-sequence typing (MLST). Interestingly, the majority of strains were multidrug-resistant and carried the blaNDM gene. A large part was characterized by a multireplicon status, and FII, A/C, FIA (15%) was the predominant. Despite the limited size of collection, MLST analysis revealed a high number of Sequence Types (STs): 14 STs among 28 K. pneumoniae and 8 STs among 11 E. coli, with the prevalence of the well-known clones ST307 and ST131, respectively. This issue indicated that some strains shared the same circulating clone. We identified a novel, so far never described, ST named ST10555, found in one E. coli strain. Our investigation showed a high heterogeneity of CPE circulating among neonatal units, confirming the need to monitor their dissemination in the hospital also through molecular methods.
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Affiliation(s)
- Marilena Agosta
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.A.); (M.A.); (L.P.); (A.S.); (C.F.P.)
| | - Daniela Bencardino
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, 61032 Fano, Italy; (D.B.); (M.M.); (F.A.)
| | - Marta Argentieri
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.A.); (M.A.); (L.P.); (A.S.); (C.F.P.)
| | - Laura Pansani
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.A.); (M.A.); (L.P.); (A.S.); (C.F.P.)
| | - Annamaria Sisto
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.A.); (M.A.); (L.P.); (A.S.); (C.F.P.)
| | - Marta Luisa Ciofi Degli Atti
- Clinical Pathways and Epidemiology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.L.C.D.A.); (C.D.)
| | - Carmen D’Amore
- Clinical Pathways and Epidemiology Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.L.C.D.A.); (C.D.)
| | - Lorenza Putignani
- Human Microbiome Unit, Department of Diagnostics and Laboratory Medicine, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Pietro Bagolan
- Neonatal Surgery Unit, Medical and Surgical Department of the Fetus-Newborn-Infant, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (P.B.); (B.D.I.)
| | - Barbara Daniela Iacobelli
- Neonatal Surgery Unit, Medical and Surgical Department of the Fetus-Newborn-Infant, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (P.B.); (B.D.I.)
| | - Andrea Dotta
- Neonatal Intensive Care Unit, Medical and Surgical Department of the Fetus-Newborn-Infant, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (A.D.); (L.M.)
| | - Ludovica Martini
- Neonatal Intensive Care Unit, Medical and Surgical Department of the Fetus-Newborn-Infant, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (A.D.); (L.M.)
| | - Luca Di Chiara
- Pediatric Cardiac Intensive Care Unit, Department of Cardiology and Cardiac Surgery, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, 61032 Fano, Italy; (D.B.); (M.M.); (F.A.)
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.A.); (M.A.); (L.P.); (A.S.); (C.F.P.)
| | - Francesca Andreoni
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, 61032 Fano, Italy; (D.B.); (M.M.); (F.A.)
| | - Paola Bernaschi
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (M.A.); (M.A.); (L.P.); (A.S.); (C.F.P.)
- Correspondence: ; Tel.: +39-06-6859-2205
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8
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Xia H, Horn J, Piotrowska MJ, Sakowski K, Karch A, Tahir H, Kretzschmar M, Mikolajczyk R. Effects of incomplete inter-hospital network data on the assessment of transmission dynamics of hospital-acquired infections. PLoS Comput Biol 2021; 17:e1008941. [PMID: 33956787 PMCID: PMC8130968 DOI: 10.1371/journal.pcbi.1008941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 05/18/2021] [Accepted: 04/06/2021] [Indexed: 11/25/2022] Open
Abstract
In the year 2020, there were 105 different statutory insurance companies in Germany with heterogeneous regional coverage. Obtaining data from all insurance companies is challenging, so that it is likely that projects will have to rely on data not covering the whole population. Consequently, the study of epidemic spread in hospital referral networks using data-driven models may be biased. We studied this bias using data from three German regional insurance companies covering four federal states: AOK (historically “general local health insurance company”, but currently only the abbreviation is used) Lower Saxony (in Federal State of Lower Saxony), AOK Bavaria (in Bavaria), and AOK PLUS (in Thuringia and Saxony). To understand how incomplete data influence network characteristics and related epidemic simulations, we created sampled datasets by randomly dropping a proportion of patients from the full datasets and replacing them with random copies of the remaining patients to obtain scale-up datasets to the original size. For the sampled and scale-up datasets, we calculated several commonly used network measures, and compared them to those derived from the original data. We found that the network measures (degree, strength and closeness) were rather sensitive to incompleteness. Infection prevalence as an outcome from the applied susceptible-infectious-susceptible (SIS) model was fairly robust against incompleteness. At incompleteness levels as high as 90% of the original datasets the prevalence estimation bias was below 5% in scale-up datasets. Consequently, a coverage as low as 10% of the local population of the federal state population was sufficient to maintain the relative bias in prevalence below 10% for a wide range of transmission parameters as encountered in clinical settings. Our findings are reassuring that despite incomplete coverage of the population, German health insurance data can be used to study effects of patient traffic between institutions on the spread of pathogens within healthcare networks. Patterns of patients’ transfer between different hospitals contribute crucially to the risk of hospital-acquired infections (HAIs) in the health care system. To quantify this risk, network models can be applied. The estimated risk can be inaccurate in the case of incomplete data on hospital admissions, which can be a consequence of the multiplicity of insurance companies as it is the case in Germany. To develop a better understanding of how incompleteness of data affects network measures and the simulated spread of HAI, we compared those measures derived from sampled, scale-up and original data, based on hospitalization data from three AOK insurance companies. We found that common network measures were affected by incompleteness, but the simulated prevalence as a measure of epidemic spread in the network was robust over a large range of incompleteness proportions. Epidemics and the transition of the infectious diseases may be modelled on hospital data with a coverage as low as 10% of the local population, whilst maintaining accuracy to within 10% of the true population prevalence.
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Affiliation(s)
- Hanjue Xia
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Halle, Saxony-Anhalt, Germany
| | - Johannes Horn
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Halle, Saxony-Anhalt, Germany
| | - Monika J. Piotrowska
- Institute of Applied Mathematics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Konrad Sakowski
- Institute of Applied Mathematics and Mechanics, University of Warsaw, Warsaw, Poland
- Institute of High Pressure Physics, Polish Academy of Sciences, Warsaw, Poland
| | - André Karch
- Institute for Epidemiology and Social Medicine, University of Münster, Münster, North Rhine-Westphalia, Germany
| | - Hannan Tahir
- Julius Center for Health Sciences & Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mirjam Kretzschmar
- Julius Center for Health Sciences & Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Halle, Saxony-Anhalt, Germany
- * E-mail:
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9
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Suwono B, Eckmanns T, Kaspar H, Merle R, Zacher B, Kollas C, Weiser AA, Noll I, Feig M, Tenhagen BA. Cluster analysis of resistance combinations in Escherichia coli from different human and animal populations in Germany 2014-2017. PLoS One 2021; 16:e0244413. [PMID: 33471826 PMCID: PMC7817003 DOI: 10.1371/journal.pone.0244413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/09/2020] [Indexed: 11/18/2022] Open
Abstract
Recent findings on Antibiotic Resistance (AR) have brought renewed attention to the comparison of data on AR from human and animal sectors. This is however a major challenge since the data is not harmonized. This study performs a comparative analysis of data on resistance combinations in Escherichia coli (E. coli) from different routine surveillance and monitoring systems for human and different animal populations in Germany. Data on E. coli isolates were collected between 2014 and 2017 from human clinical isolates, non-clinical animal isolates from food-producing animals and food, and clinical animal isolates from food-producing and companion animals from national routine surveillance and monitoring for AR in Germany. Sixteen possible resistance combinations to four antibiotics—ampicillin, cefotaxime, ciprofloxacin and gentamicin–for these populations were used for hierarchical clustering (Euclidian and average distance). All analyses were performed with the software R 3.5.1 (Rstudio 1.1.442). Data of 333,496 E. coli isolates and forty-one different human and animal populations were included in the cluster analysis. Three main clusters were detected. Within these three clusters, all human populations (intensive care unit (ICU), general ward and outpatient care) showed similar relative frequencies of the resistance combinations and clustered together. They demonstrated similarities with clinical isolates from different animal populations and most isolates from pigs from both non-clinical and clinical isolates. Isolates from healthy poultry demonstrated similarities in relative frequencies of resistance combinations and clustered together. However, they clustered separately from the human isolates. All isolates from different animal populations with low relative frequencies of resistance combinations clustered together. They also clustered separately from the human populations. Cluster analysis has been able to demonstrate the linkage among human isolates and isolates from various animal populations based on the resistance combinations. Further analyses based on these findings might support a better one-health approach for AR in Germany.
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Affiliation(s)
- Beneditta Suwono
- Department Biological Safety, Unit Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment, Berlin, Germany
- Department Infectious Disease Epidemiology, Unit Healthcare-associated Infections, Surveillance for Antibiotic Resistance and Consumption, Robert Koch Institute, Berlin, Germany
| | - Tim Eckmanns
- Department Infectious Disease Epidemiology, Unit Healthcare-associated Infections, Surveillance for Antibiotic Resistance and Consumption, Robert Koch Institute, Berlin, Germany
| | - Heike Kaspar
- Unit Antibiotic Resistance Monitoring, Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Roswitha Merle
- Department of Veterinary Medicine, Institute for Veterinary Epidemiology and Biostatistics, Working Group Applied Epidemiology, Free University Berlin, Berlin, Germany
| | - Benedikt Zacher
- Department Infectious Disease Epidemiology, Unit Healthcare-associated Infections, Surveillance for Antibiotic Resistance and Consumption, Robert Koch Institute, Berlin, Germany
| | - Chris Kollas
- Department Biological Safety, Unit Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Armin A. Weiser
- Department Biological Safety, Unit Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Ines Noll
- Department Infectious Disease Epidemiology, Unit Healthcare-associated Infections, Surveillance for Antibiotic Resistance and Consumption, Robert Koch Institute, Berlin, Germany
| | - Marcel Feig
- Department Infectious Disease Epidemiology, Unit Healthcare-associated Infections, Surveillance for Antibiotic Resistance and Consumption, Robert Koch Institute, Berlin, Germany
| | - Bernd-Alois Tenhagen
- Department Biological Safety, Unit Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment, Berlin, Germany
- * E-mail:
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10
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Bower CW, Fridkin DW, Wolford HM, Slayton RB, Kubes JN, Jacob JT, Ray SM, Fridkin SK. Evaluating Movement of Patients With Carbapenem-resistant Enterobacteriaceae Infections in the Greater Atlanta Metropolitan Area Using Social Network Analysis. Clin Infect Dis 2021; 70:75-81. [PMID: 30809636 DOI: 10.1093/cid/ciz154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/20/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacteriaceae (CRE) are an urgent threat with potential for rapid spread. We evaluated the role of Medicare patient movement between facilities to model the spread of CRE within a region. METHODS Through population-based CRE surveillance in the 8-county Atlanta (GA) metropolitan area, all Escherichia coli, Enterobacter spp., or Klebsiella spp. resistant to ≥1 carbapenem were reported from residents. CRE was attributed to a facility based on timing of culture and facility exposures. Centrality metrics were calculated from 2016 Medicare data and compared to CRE-transfer derived centrality metrics by Spearman correlation. RESULTS During 2016, 283 incident CRE cases with concurrent or prior year facility stays were identified; cases were attributed mostly to acute care hospitals (ACHs; 141, 50%) and skilled nursing facilities (SNFs; 113, 40%), and less frequently to long-term acute care hospitals (LTACHs; 29, 10%). Attribution was widespread, originating at 17 of 20 ACHs (85%), 7 of 8 (88%) LTACHs, but only 35 of 65 (54%) SNFs. Betweenness of Medicare patient transfers strongly correlated with betweenness of CRE case-transfer data in ACHs (r = 0.75; P < .01) and LTACHs (r = 0.77; P = .03), but not in SNFs (r = 0.02; P = 0.85). We noted 6 SNFs with high CRE-derived betweenness but low Medicare-derived betweenness. CONCLUSIONS CRE infections originate from almost all ACHs and half of SNFs. We identified a subset of SNFs central to the CRE transfer network but not the Medicare transfer network; other factors may explain CRE patient movement in these facilities.
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Affiliation(s)
- Chris W Bower
- Georgia Emerging Infections Program, Atlanta, Georgia.,Atlanta Veterans Affairs Medical Center, Decatur, Atlanta, Georgia.,Atlanta Research and Education Foundation, Atlanta, Georgia
| | - Daniel W Fridkin
- Georgia Emerging Infections Program, Atlanta, Georgia.,Atlanta Veterans Affairs Medical Center, Decatur, Atlanta, Georgia.,Atlanta Research and Education Foundation, Atlanta, Georgia
| | - Hannah M Wolford
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Rachel B Slayton
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Julianne N Kubes
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Jesse T Jacob
- Georgia Emerging Infections Program, Atlanta, Georgia.,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Susan M Ray
- Georgia Emerging Infections Program, Atlanta, Georgia.,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Scott K Fridkin
- Georgia Emerging Infections Program, Atlanta, Georgia.,Atlanta Veterans Affairs Medical Center, Decatur, Atlanta, Georgia.,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
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11
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Modelling pathogen spread in a healthcare network: Indirect patient movements. PLoS Comput Biol 2020; 16:e1008442. [PMID: 33253154 PMCID: PMC7728397 DOI: 10.1371/journal.pcbi.1008442] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 12/10/2020] [Accepted: 10/16/2020] [Indexed: 11/28/2022] Open
Abstract
Inter-hospital patient transfers (direct transfers) between healthcare facilities have been shown to contribute to the spread of pathogens in a healthcare network. However, the impact of indirect transfers (patients re-admitted from the community to the same or different hospital) is not well studied. This work aims to study the contribution of indirect transfers to the spread of pathogens in a healthcare network. To address this aim, a hybrid network–deterministic model to simulate the spread of multiresistant pathogens in a healthcare system was developed for the region of Lower Saxony (Germany). The model accounts for both, direct and indirect transfers of patients. Intra-hospital pathogen transmission is governed by a SIS model expressed by a system of ordinary differential equations. Our results show that the proposed model reproduces the basic properties of healthcare-associated pathogen spread. They also show the importance of indirect transfers: restricting the pathogen spread to direct transfers only leads to 4.2% system wide prevalence. However, adding indirect transfers leads to an increase in the overall prevalence by a factor of 4 (18%). In addition, we demonstrated that the final prevalence in the individual healthcare facilities depends on average length of stay in a way described by a non-linear concave function. Moreover, we demonstrate that the network parameters of the model may be derived from administrative admission/discharge records. In particular, they are sufficient to obtain inter-hospital transfer probabilities, and to express the patients’ transfers as a Markov process. Using the proposed model, we show that indirect transfers of patients are equally or even more important as direct transfers for the spread of pathogens in a healthcare network. Direct patient transfers between hospitals have been shown to play an important role in the spread of pathogens in a healthcare network. However, readmission of patients from the community (indirect transfers) to the same or a different hospital is not well studied, and its role for the spread of pathogens in a healthcare network is not quantified. In this work, we developed a network model of a healthcare system to study the impact of indirect transfers on the prevalence in the individual hospitals as well as in the overall healthcare system. The model includes both, direct and indirect transfers of patients between the healthcare facilities due to transferring as well as readmission of infectious (colonized or infected) patients. Our results show that the readmission of patients (indirect transfers), either to the same or different facility, is an important potential channel of pathogen transmission. Such indirect transfers are of no less importance than direct patient transfers in controlling the spread of pathogens in a healthcare network.
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12
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Haque M, McKimm J, Sartelli M, Dhingra S, Labricciosa FM, Islam S, Jahan D, Nusrat T, Chowdhury TS, Coccolini F, Iskandar K, Catena F, Charan J. Strategies to Prevent Healthcare-Associated Infections: A Narrative Overview. Risk Manag Healthc Policy 2020; 13:1765-1780. [PMID: 33061710 PMCID: PMC7532064 DOI: 10.2147/rmhp.s269315] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/09/2020] [Indexed: 12/13/2022] Open
Abstract
Healthcare-associated infections (HCAIs) are a major source of morbidity and mortality and are the second most prevalent cause of death. Furthermore, it has been reported that for every one-hundred patients admitted to hospital, seven patients in high-income economies and ten in emerging and low-income economies acquire at least one type of HCAI. Currently, almost all pathogenic microorganisms have developed antimicrobial resistance, and few new antimicrobials are being developed and brought to market. The literature search for this narrative review was performed by searching bibliographic databases (including Google Scholar and PubMed) using the search terms: "Strategies," "Prevention," and "Healthcare-Associated Infections," followed by snowballing references cited by critical articles. We found that although hand hygiene is a centuries-old concept, it is still the primary strategy used around the world to prevent HCAIs. It forms one of a bundle of approaches used to clean and maintain a safe hospital environment and to stop the transmission of contagious and infectious microorganisms, including multidrug-resistant microbes. Finally, antibiotic stewardship also has a crucial role in reducing the impact of HCAIs through conserving currently available antimicrobials.
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Affiliation(s)
- Mainul Haque
- Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur57000, Malaysia
| | - Judy McKimm
- Medical Education, Swansea University School of Medicine, Grove Building, Swansea University, Swansea, WalesSA2 8PP, UK
| | - Massimo Sartelli
- Department of General and Emergency Surgery, Macerata Hospital, Macerata, Italy
| | - Sameer Dhingra
- School of Pharmacy, The University of the West Indies, St. Augustine Campus, Faculty of Medical Sciences, Eric Williams Medical Sciences Complex, Uriah Butler Highway, Trinidad & Tobago, West Indies
| | | | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka1342, Bangladesh
| | - Dilshad Jahan
- Department of Hematology, Asgar Ali Hospital, Dhaka1204, Bangladesh
| | - Tanzina Nusrat
- Department of Microbiology, Chittagong Medical College, Chattogram4203, Bangladesh
| | | | - Federico Coccolini
- Department of General Emergency and Trauma Surgery, Pisa University Hospital, Pisa, Italy
| | - Katia Iskandar
- School of Pharmacy, Lebanese University, Beirut, Lebanon
| | - Fausto Catena
- Department of Emergency Surgery, Parma Maggiore Hospital, Parma, Italy
| | - Jaykaran Charan
- Department of Pharmacology, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
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13
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Fridkin SK. Advances in Data-Driven Responses to Preventing Spread of Antibiotic Resistance Across Health-Care Settings. Epidemiol Rev 2020; 41:6-12. [PMID: 31673712 DOI: 10.1093/epirev/mxz010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 05/08/2019] [Accepted: 09/13/2019] [Indexed: 12/25/2022] Open
Abstract
Among the most urgent and serious threats to public health are 7 antibiotic-resistant bacterial infections predominately acquired during health-care delivery. There is an emerging field of health-care epidemiology that is focused on preventing health care-associated infections with antibiotic-resistant bacteria and incorporates data from patient transfers or patient movements within and between facilities. This analytic field is being used to help public health professionals identify best opportunities for prevention. Different analytic approaches that draw on uses of big data are being explored to help target the use of limited public health resources, leverage expertise, and enact effective policy to maximize an impact on population-level health. Here, the following recent advances in data-driven responses to preventing spread of antibiotic resistance across health-care settings are summarized: leveraging big data for machine learning, integration or advances in tracking patient movement, and highlighting the value of coordinating response across institutions within a region.
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Affiliation(s)
- Scott K Fridkin
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia.,Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
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14
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Nguyen LKN, Megiddo I, Howick S. Simulation models for transmission of health care-associated infection: A systematic review. Am J Infect Control 2020; 48:810-821. [PMID: 31862167 PMCID: PMC7161411 DOI: 10.1016/j.ajic.2019.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND Health care-associated infections (HAIs) are a global health burden because of their significant impact on patient health and health care systems. Mechanistic simulation modeling that captures the dynamics between patients, pathogens, and the environment is increasingly being used to improve understanding of epidemiological patterns of HAIs and to facilitate decisions on infection prevention and control (IPC). The purpose of this review is to present a systematic review to establish (1) how simulation models have been used to investigate HAIs and their mitigation and (2) how these models have evolved over time, as well as identify (3) gaps in their adoption and (4) useful directions for their future development. METHODS The review involved a systematic search and identification of studies using system dynamics, discrete event simulation, and agent-based model to study HAIs. RESULTS The complexity of simulation models developed for HAIs significantly increased but heavily concentrated on transmission dynamics of methicillin-resistant Staphylococcus aureus in the hospitals of high-income countries. Neither HAIs in other health care settings, the influence of contact networks within a health care facility, nor patient sharing and referring networks across health care settings were sufficiently understood. CONCLUSIONS This systematic review provides a broader overview of existing simulation models in HAIs to identify the gaps and to direct and facilitate further development of appropriate models in this emerging field.
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Affiliation(s)
- Le Khanh Ngan Nguyen
- Department of Management Science, Cathedral Wing, Strathclyde Business School, University of Strathclyde, Glasgow, United Kingdom.
| | - Itamar Megiddo
- Department of Management Science, Cathedral Wing, Strathclyde Business School, University of Strathclyde, Glasgow, United Kingdom
| | - Susan Howick
- Department of Management Science, Cathedral Wing, Strathclyde Business School, University of Strathclyde, Glasgow, United Kingdom
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15
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Prevention and Control of Multidrug-Resistant Bacteria in The Netherlands and Germany-The Impact of Healthcare Structures. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17072337. [PMID: 32235650 PMCID: PMC7178045 DOI: 10.3390/ijerph17072337] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 03/28/2020] [Accepted: 03/29/2020] [Indexed: 11/23/2022]
Abstract
The Netherlands and Germany are neighbouring countries within the European Union but are differently affected by multidrug-resistant microorganisms (MDRO). In this narrative review, we summarize data about antibiotic use, the occurrence of MDRO and healthcare-associated infections in these two countries, as well as data about organizational and structural differences between the Dutch and German healthcare systems. These results are discussed with a focus on whether or how the organization of healthcare influences MDRO prevention. We found that from the point of view of MDRO prevention, a higher density of inpatient care, a higher number of hospitals, a longer length of stay and lower staffing ratios might facilitate MDRO dissemination in German hospitals.
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16
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Bastard J, Andraud M, Chauvin C, Glaser P, Opatowski L, Temime L. Dynamics of livestock-associated methicillin resistant Staphylococcus aureus in pig movement networks: Insight from mathematical modeling and French data. Epidemics 2020; 31:100389. [PMID: 32146319 DOI: 10.1016/j.epidem.2020.100389] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/17/2019] [Accepted: 02/07/2020] [Indexed: 12/15/2022] Open
Abstract
Livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) colonizes livestock animals worldwide, especially pigs and calves. Although frequently carried asymptomatically, LA-MRSA can cause severe infections in humans. It is therefore important to better understand LA-MRSA spreading dynamics within pig farms and over pig movement networks, and to compare different strategies of control and surveillance. For this purpose, we propose a stochastic meta-population model of LA-MRSA spread along the French pig movement network (n = 10,542 farms), combining within- and between-farm dynamics, based on detailed data on breeding practices and pig movements between holdings. We calibrate the model using French epidemiological data. We then identify farm-level factors associated with the spreading potential of LA-MRSA in the network. We also show that, assuming control measures applied in a limited (n = 100) number of farms, targeting farms depending on their centrality in the network is the only way to significantly reduce LA-MRSA global prevalence. Finally, we investigate the scenario of emergence of a new LA-MRSA strain, and find that the farms with the highest indegree would be the best sentinels for a targeted surveillance of such a strain's introduction.
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Affiliation(s)
- Jonathan Bastard
- Université Paris-Saclay, UVSQ, Univ. Paris-Sud, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, F-78180, Montigny-Le-Bretonneux, France; Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion unit, F-75015, Paris, France; MESuRS Laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003 Paris, France; PACRI Unit, Conservatoire National des Arts et Métiers, Institut Pasteur, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
| | - Mathieu Andraud
- Ploufragan Plouzané Niort Laboratory, Epidemiology, Health and Welfare Research Unit, Anses, BP 53, 22440 Ploufragan, France; Université Bretagne Loire, Cité internationale, 1 place Paul Ricoeur CS 54417, 35044 Rennes, France
| | - Claire Chauvin
- Ploufragan Plouzané Niort Laboratory, Epidemiology, Health and Welfare Research Unit, Anses, BP 53, 22440 Ploufragan, France; Université Bretagne Loire, Cité internationale, 1 place Paul Ricoeur CS 54417, 35044 Rennes, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotics Resistance (EERA) Unit, CNRS UMR 3525, Institut Pasteur, AP-HP, Université Paris-Sud, 28 Rue du Docteur Roux, 75015 Paris, France
| | - Lulla Opatowski
- Université Paris-Saclay, UVSQ, Univ. Paris-Sud, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, F-78180, Montigny-Le-Bretonneux, France; Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion unit, F-75015, Paris, France
| | - Laura Temime
- MESuRS Laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003 Paris, France; PACRI Unit, Conservatoire National des Arts et Métiers, Institut Pasteur, Paris, France
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17
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Ray MJ, Lin MY, Tang AS, Arwady MA, Lavin MA, Runningdeer E, Jovanov D, Trick WE. Regional Spread of an Outbreak of Carbapenem-Resistant Enterobacteriaceae Through an Ego Network of Healthcare Facilities. Clin Infect Dis 2019; 67:407-410. [PMID: 29415264 DOI: 10.1093/cid/ciy084] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/01/2018] [Indexed: 01/26/2023] Open
Abstract
Background In 2013, New Delhi metallo-β-lactamase (NDM)-producing Escherichia coli, a type of carbapenem-resistant Enterobacteriaceae uncommon in the United States, was identified in a tertiary care hospital (hospital A) in northeastern Illinois. The outbreak was traced to a contaminated duodenoscope. Patient-sharing patterns can be described through social network analysis and ego networks, which could be used to identify hospitals most likely to accept patients from a hospital with an outbreak. Methods Using Illinois' hospital discharge data and the Illinois extensively drug-resistant organism (XDRO) registry, we constructed an ego network around hospital A. We identified which facilities NDM outbreak patients subsequently visited and whether the facilities reported NDM cases. Results Of the 31 outbreak cases entered into the XDRO registry who visited hospital A, 19 (61%) were subsequently admitted to 13 other hospitals during the following 12 months. Of the 13 hospitals, the majority (n = 9; 69%) were in our defined ego network, and 5 of those 9 hospitals consequently reported at least 1 additional NDM case. Ego network facilities were more likely to identify cases compared to a geographically defined group of facilities (9/22 vs 10/66; P = .01); only 1 reported case fell outside of the ego network. Conclusions The outbreak hospital's ego network accurately predicted which hospitals the outbreak patients would visit. Many of these hospitals reported additional NDM cases. Prior knowledge of this ego network could have efficiently focused public health resources on these high-risk facilities.
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Affiliation(s)
- Michael J Ray
- Cook County Health and Hospitals System, Chicago.,Hektoen Institute of Medicine, Chicago
| | | | | | | | | | | | | | - William E Trick
- Cook County Health and Hospitals System, Chicago.,Rush University Medical Center, Chicago
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18
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Pei S, Morone F, Liljeros F, Makse H, Shaman JL. Inference and control of the nosocomial transmission of methicillin-resistant Staphylococcus aureus. eLife 2018; 7:e40977. [PMID: 30560786 PMCID: PMC6298769 DOI: 10.7554/elife.40977] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/16/2018] [Indexed: 12/19/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a continued threat to human health in both community and healthcare settings. In hospitals, control efforts would benefit from accurate estimation of asymptomatic colonization and infection importation rates from the community. However, developing such estimates remains challenging due to limited observation of colonization and complicated transmission dynamics within hospitals and the community. Here, we develop an inference framework that can estimate these key quantities by combining statistical filtering techniques, an agent-based model, and real-world patient-to-patient contact networks, and use this framework to infer nosocomial transmission and infection importation over an outbreak spanning 6 years in 66 Swedish hospitals. In particular, we identify a small number of patients with disproportionately high risk of colonization. In retrospective control experiments, interventions targeted to these individuals yield a substantial improvement over heuristic strategies informed by number of contacts, length of stay and contact tracing.
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Affiliation(s)
- Sen Pei
- Department of Environmental Health Sciences, Mailman School of Public HealthColumbia UniversityNew YorkUnited States
| | - Flaviano Morone
- Levich Institute and Physics DepartmentCity College of New YorkNew YorkUnited States
| | | | - Hernán Makse
- Levich Institute and Physics DepartmentCity College of New YorkNew YorkUnited States
| | - Jeffrey L Shaman
- Department of Environmental Health Sciences, Mailman School of Public HealthColumbia UniversityNew YorkUnited States
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19
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Kirtikliene T, Naugzemys D, Steponkiene A, Bogdevic R, Vizuje G, Zvingila D, Kuisiene N. Evaluation of the Inter- and Intrahospital Spread of Multidrug Resistant Gram-Negative Bacteria in Lithuanian Hospitals. Microb Drug Resist 2018; 25:326-335. [PMID: 30339100 DOI: 10.1089/mdr.2018.0160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Spread of multidrug-resistant pathogenic bacteria became one of the greatest threats in healthcare worldwide. It is generally accepted that both inter- and intrahospital transmissions of these bacteria contribute significantly to this problem. The purpose of the current study was the evaluation of the inter- and intrahospital spread of multidrug resistant Gram-negative pathogenic bacteria in Lithuania. Clinical isolates of Acinetobacter sp., Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa were subjected for the screening for extended spectrum β-lactamase, carbapenemase, as well as plasmid-mediated AmpC β-lactamase genes. BOX-PCR genotyping was used for the genotyping of these isolates. Our results show that all four pathogens are involved in the intra- and/or interhospital dissemination between the Lithuanian healthcare institutions. The level of transmissions differed between pathogens, and the worst situation was detected for Acinetobacter sp. followed by E. coli. In almost all cases, transmissible strains had at least one gene conferring β-lactam resistance, thereby contributing to the dissemination of the resistance determinants in and between Lithuanian hospitals. Our study clearly demonstrated that immediate actions, more effective strategy, and surveillance are needed to confine and prevent further spread of multidrug resistant Gram-negative pathogenic bacteria in Lithuanian healthcare institutions.
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Affiliation(s)
- Tatjana Kirtikliene
- 1 Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University , Vilnius, Lithuania .,2 Department of Clinical Testing , National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Donatas Naugzemys
- 3 Botanical Garden of Vilnius University, Vilnius University , Vilnius, Lithuania
| | - Ana Steponkiene
- 2 Department of Clinical Testing , National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Robert Bogdevic
- 2 Department of Clinical Testing , National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Greta Vizuje
- 2 Department of Clinical Testing , National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Donatas Zvingila
- 4 Department of Botany and Genetics, Institute of Biosciences, Life Sciences Center, Vilnius University , Vilnius, Lithuania
| | - Nomeda Kuisiene
- 1 Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University , Vilnius, Lithuania
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Snitkin ES, Won S, Pirani A, Lapp Z, Weinstein RA, Lolans K, Hayden MK. Integrated genomic and interfacility patient-transfer data reveal the transmission pathways of multidrug-resistant Klebsiella pneumoniae in a regional outbreak. Sci Transl Med 2018; 9:9/417/eaan0093. [PMID: 29167391 DOI: 10.1126/scitranslmed.aan0093] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/16/2017] [Accepted: 08/18/2017] [Indexed: 12/15/2022]
Abstract
Development of effective strategies to limit the proliferation of multidrug-resistant organisms requires a thorough understanding of how such organisms spread among health care facilities. We sought to uncover the chains of transmission underlying a 2008 U.S. regional outbreak of carbapenem-resistant Klebsiella pneumoniae by performing an integrated analysis of genomic and interfacility patient-transfer data. Genomic analysis yielded a high-resolution transmission network that assigned directionality to regional transmission events and discriminated between intra- and interfacility transmission when epidemiologic data were ambiguous or misleading. Examining the genomic transmission network in the context of interfacility patient transfers (patient-sharing networks) supported the role of patient transfers in driving the outbreak, with genomic analysis revealing that a small subset of patient-transfer events was sufficient to explain regional spread. Further integration of the genomic and patient-sharing networks identified one nursing home as an important bridge facility early in the outbreak-a role that was not apparent from analysis of genomic or patient-transfer data alone. Last, we found that when simulating a real-time regional outbreak, our methodology was able to accurately infer the facility at which patients acquired their infections. This approach has the potential to identify facilities with high rates of intra- or interfacility transmission, data that will be useful for triggering targeted interventions to prevent further spread of multidrug-resistant organisms.
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Affiliation(s)
- Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA. .,Division of Infectious Diseases, Department of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Won
- Division of Infectious Diseases, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
| | - Ali Pirani
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.,Division of Infectious Diseases, Department of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zena Lapp
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert A Weinstein
- Division of Infectious Diseases, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA.,Division of Infectious Diseases, Department of Medicine, Cook County Health and Hospitals System, Chicago, IL 60612, USA
| | - Karen Lolans
- Division of Clinical Microbiology, Department of Pathology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA. .,Division of Clinical Microbiology, Department of Pathology, Rush University Medical Center, Chicago, IL 60612, USA
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Brunson JC, Laubenbacher RC. Applications of network analysis to routinely collected health care data: a systematic review. J Am Med Inform Assoc 2018; 25:210-221. [PMID: 29025116 PMCID: PMC6664849 DOI: 10.1093/jamia/ocx052] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/18/2017] [Accepted: 04/23/2017] [Indexed: 01/21/2023] Open
Abstract
Objective To survey network analyses of datasets collected in the course of routine operations in health care settings and identify driving questions, methods, needs, and potential for future research. Materials and Methods A search strategy was designed to find studies that applied network analysis to routinely collected health care datasets and was adapted to 3 bibliographic databases. The results were grouped according to a thematic analysis of their settings, objectives, data, and methods. Each group received a methodological synthesis. Results The search found 189 distinct studies reported before August 2016. We manually partitioned the sample into 4 groups, which investigated institutional exchange, physician collaboration, clinical co-occurrence, and workplace interaction networks. Several robust and ongoing research programs were discerned within (and sometimes across) the groups. Little interaction was observed between these programs, despite conceptual and methodological similarities. Discussion We use the literature sample to inform a discussion of good practice at this methodological interface, including the concordance of motivations, study design, data, and tools and the validation and standardization of techniques. We then highlight instances of positive feedback between methodological development and knowledge domains and assess the overall cohesion of the sample.
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Mathematical models of infection transmission in healthcare settings: recent advances from the use of network structured data. Curr Opin Infect Dis 2018; 30:410-418. [PMID: 28570284 DOI: 10.1097/qco.0000000000000390] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
PURPOSE OF REVIEW Mathematical modeling approaches have brought important contributions to the study of pathogen spread in healthcare settings over the last 20 years. Here, we conduct a comprehensive systematic review of mathematical models of disease transmission in healthcare settings and assess the application of contact and patient transfer network data over time and their impact on our understanding of transmission dynamics of infections. RECENT FINDINGS Recently, with the increasing availability of data on the structure of interindividual and interinstitution networks, models incorporating this type of information have been proposed, with the aim of providing more realistic predictions of disease transmission in healthcare settings. Models incorporating realistic data on individual or facility networks often remain limited to a few settings and a few pathogens (mostly methicillin-resistant Staphylococcus aureus). SUMMARY To respond to the objectives of creating improved infection prevention and control measures and better understanding of healthcare-associated infections transmission dynamics, further innovations in data collection and parameter estimation in modeling is required.
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Herzog SA, Blaizot S, Hens N. Mathematical models used to inform study design or surveillance systems in infectious diseases: a systematic review. BMC Infect Dis 2017; 17:775. [PMID: 29254504 PMCID: PMC5735541 DOI: 10.1186/s12879-017-2874-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/30/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Mathematical models offer the possibility to investigate the infectious disease dynamics over time and may help in informing design of studies. A systematic review was performed in order to determine to what extent mathematical models have been incorporated into the process of planning studies and hence inform study design for infectious diseases transmitted between humans and/or animals. METHODS We searched Ovid Medline and two trial registry platforms (Cochrane, WHO) using search terms related to infection, mathematical model, and study design from the earliest dates to October 2016. Eligible publications and registered trials included mathematical models (compartmental, individual-based, or Markov) which were described and used to inform the design of infectious disease studies. We extracted information about the investigated infection, population, model characteristics, and study design. RESULTS We identified 28 unique publications but no registered trials. Focusing on compartmental and individual-based models we found 12 observational/surveillance studies and 11 clinical trials. Infections studied were equally animal and human infectious diseases for the observational/surveillance studies, while all but one between humans for clinical trials. The mathematical models were used to inform, amongst other things, the required sample size (n = 16), the statistical power (n = 9), the frequency at which samples should be taken (n = 6), and from whom (n = 6). CONCLUSIONS Despite the fact that mathematical models have been advocated to be used at the planning stage of studies or surveillance systems, they are used scarcely. With only one exception, the publications described theoretical studies, hence, not being utilised in real studies.
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Affiliation(s)
- Sereina A. Herzog
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Stéphanie Blaizot
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Niel Hens
- Centre for Health Economics Research and Modelling Infectious Diseases (CHERMID), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Hasselt University, Hasselt, Belgium
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Nekkab N, Astagneau P, Temime L, Crépey P. Spread of hospital-acquired infections: A comparison of healthcare networks. PLoS Comput Biol 2017; 13:e1005666. [PMID: 28837555 PMCID: PMC5570216 DOI: 10.1371/journal.pcbi.1005666] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/03/2017] [Indexed: 11/20/2022] Open
Abstract
Hospital-acquired infections (HAIs), including emerging multi-drug resistant organisms, threaten healthcare systems worldwide. Efficient containment measures of HAIs must mobilize the entire healthcare network. Thus, to best understand how to reduce the potential scale of HAI epidemic spread, we explore patient transfer patterns in the French healthcare system. Using an exhaustive database of all hospital discharge summaries in France in 2014, we construct and analyze three patient networks based on the following: transfers of patients with HAI (HAI-specific network); patients with suspected HAI (suspected-HAI network); and all patients (general network). All three networks have heterogeneous patient flow and demonstrate small-world and scale-free characteristics. Patient populations that comprise these networks are also heterogeneous in their movement patterns. Ranking of hospitals by centrality measures and comparing community clustering using community detection algorithms shows that despite the differences in patient population, the HAI-specific and suspected-HAI networks rely on the same underlying structure as that of the general network. As a result, the general network may be more reliable in studying potential spread of HAIs. Finally, we identify transfer patterns at both the French regional and departmental (county) levels that are important in the identification of key hospital centers, patient flow trajectories, and regional clusters that may serve as a basis for novel wide-scale infection control strategies. Hospital-acquired infections (HAIs), including emerging multi-drug resistant organisms, threaten healthcare systems worldwide. Efficient containment measures of HAIs must mobilize the entire healthcare network. Thus, to best understand how to reduce the scale of potential HAI epidemic spread, we explore patient transfer patterns in the French healthcare system. We construct and compare the characteristics of three different patient transfer networks based on data on transfers of patients with diagnosed HAIs, suspected HAIs, or of all patients. Our analyses show that these healthcare networks, the patient populations that comprise them and the patient movement patterns are heterogeneous and centralized. Despite the differences in patient populations, the HAI-specific and suspected-HAI healthcare networks have the same underlying structure as that of the general healthcare network. We identify key hospital centers, patient flow trajectories, at both the regional and department (county) level that may serve as a basis for proposing novel wide-scale infection control strategies.
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Affiliation(s)
- Narimane Nekkab
- Laboratoire MESuRS, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, Paris, France
- Institut Pasteur, Cnam, Unité PACRI, 25–28, rue du Docteur Roux, Paris, France
- Ecole des Hautes Etudes en Santé Publique, Département d'Epidémiologie et de Biostatistiques, 15 Avenue du Professeur-Léon-Bernard, Rennes, France
- * E-mail:
| | - Pascal Astagneau
- Ecole des Hautes Etudes en Santé Publique, Département d'Epidémiologie et de Biostatistiques, 15 Avenue du Professeur-Léon-Bernard, Rennes, France
- Centre de prévention des infections associées aux soins (C-CLIN), APHP, Paris, France
- Faculté de médecine Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Laura Temime
- Laboratoire MESuRS, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, Paris, France
- Institut Pasteur, Cnam, Unité PACRI, 25–28, rue du Docteur Roux, Paris, France
| | - Pascal Crépey
- Ecole des Hautes Etudes en Santé Publique, Département d'Epidémiologie et de Biostatistiques, 15 Avenue du Professeur-Léon-Bernard, Rennes, France
- UMR190, Emergence des Pathologies Virales, Marseille, France
- UPRES EA 7449 Reperes, Rennes, France
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25
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Measuring distance through dense weighted networks: The case of hospital-associated pathogens. PLoS Comput Biol 2017; 13:e1005622. [PMID: 28771581 PMCID: PMC5542422 DOI: 10.1371/journal.pcbi.1005622] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/13/2017] [Indexed: 12/02/2022] Open
Abstract
Hospital networks, formed by patients visiting multiple hospitals, affect the spread of hospital-associated infections, resulting in differences in risks for hospitals depending on their network position. These networks are increasingly used to inform strategies to prevent and control the spread of hospital-associated pathogens. However, many studies only consider patients that are received directly from the initial hospital, without considering the effect of indirect trajectories through the network. We determine the optimal way to measure the distance between hospitals within the network, by reconstructing the English hospital network based on shared patients in 2014–2015, and simulating the spread of a hospital-associated pathogen between hospitals, taking into consideration that each intermediate hospital conveys a delay in the further spread of the pathogen. While the risk of transferring a hospital-associated pathogen between directly neighbouring hospitals is a direct reflection of the number of shared patients, the distance between two hospitals far-away in the network is determined largely by the number of intermediate hospitals in the network. Because the network is dense, most long distance transmission chains in fact involve only few intermediate steps, spreading along the many weak links. The dense connectivity of hospital networks, together with a strong regional structure, causes hospital-associated pathogens to spread from the initial outbreak in a two-step process: first, the directly surrounding hospitals are affected through the strong connections, second all other hospitals receive introductions through the multitude of weaker links. Although the strong connections matter for local spread, weak links in the network can offer ideal routes for hospital-associated pathogens to travel further faster. This hold important implications for infection prevention and control efforts: if a local outbreak is not controlled in time, colonised patients will appear in other regions, irrespective of the distance to the initial outbreak, making import screening ever more difficult. Shared patients can spread hospital-associated pathogens between hospitals, together forming a large network in which all hospitals are connected. We set out to measure the distance between hospitals in such a network, best reflecting the risk of a hospital-associated pathogen spreading from one to the other. The central problem is that this risk may not be a directly reflected by the weight of the direct connections between hospitals, because the pathogen could arrive through a longer indirect route, first causing a problem in an intermediate hospital. We determined the optimal balance between connection weights and path length, by testing different weighting factors between them against simulated spread of a pathogen. We found that while strong connections are important risk factor for a hospital’s direct neighbours, weak connections offer ideal indirect routes for hospital-associated pathogens to travel further faster. These routes should not be underestimated when designing control strategies.
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Donker T, Henderson KL, Hopkins KL, Dodgson AR, Thomas S, Crook DW, Peto TEA, Johnson AP, Woodford N, Walker AS, Robotham JV. The relative importance of large problems far away versus small problems closer to home: insights into limiting the spread of antimicrobial resistance in England. BMC Med 2017; 15:86. [PMID: 28446169 PMCID: PMC5406888 DOI: 10.1186/s12916-017-0844-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/24/2017] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND To combat the spread of antimicrobial resistance (AMR), hospitals are advised to screen high-risk patients for carriage of antibiotic-resistant bacteria on admission. This often includes patients previously admitted to hospitals with a high AMR prevalence. However, the ability of such a strategy to identify introductions (and hence prevent onward transmission) is unclear, as it depends on AMR prevalence in each hospital, the number of patients moving between hospitals, and the number of hospitals considered 'high risk'. METHODS We tracked patient movements using data from the National Health Service of England Hospital Episode Statistics and estimated differences in regional AMR prevalences using, as an exemplar, data collected through the national reference laboratory service of Public Health England on carbapenemase-producing Enterobacteriaceae (CPE) from 2008 to 2014. Combining these datasets, we calculated expected CPE introductions into hospitals from across the hospital network to assess the effectiveness of admission screening based on defining high-prevalence hospitals as high risk. RESULTS Based on numbers of exchanged patients, the English hospital network can be divided into 14 referral regions. England saw a sharp increase in numbers of CPE isolates referred to the national reference laboratory over 7 years, from 26 isolates in 2008 to 1649 in 2014. Large regional differences in numbers of confirmed CPE isolates overlapped with regional structuring of patient movements between hospitals. However, despite these large differences in prevalence between regions, we estimated that hospitals received only a small proportion (1.8%) of CPE-colonised patients from hospitals outside their own region, which decreased over time. CONCLUSIONS In contrast to the focus on import screening based on assigning a few hospitals as 'high risk', patient transfers between hospitals with small AMR problems in the same region often pose a larger absolute threat than patient transfers from hospitals in other regions with large problems, even if the prevalence in other regions is orders of magnitude higher. Because the difference in numbers of exchanged patients, between and within regions, was mostly larger than the difference in CPE prevalence, it would be more effective for hospitals to focus on their own populations or region to inform control efforts rather than focussing on problems elsewhere.
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Affiliation(s)
- Tjibbe Donker
- The National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK. .,Nuffield Department of Medicine, University of Oxford, Oxford, UK. .,National Infection Service, Public Health England, Colindale, London, UK.
| | | | - Katie L Hopkins
- The National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,National Infection Service, Public Health England, Colindale, London, UK
| | - Andrew R Dodgson
- Public Health Laboratory, Public Health England, Manchester Royal Infirmary, Manchester, UK.,Department of Microbiology, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Stephanie Thomas
- Microbiology Department, University Hospital South Manchester, Manchester, UK
| | - Derrick W Crook
- The National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK.,National Infection Service, Public Health England, Colindale, London, UK.,NIHR Biomedical Research Centre, Oxford, UK
| | - Tim E A Peto
- The National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Biomedical Research Centre, Oxford, UK
| | - Alan P Johnson
- The National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,National Infection Service, Public Health England, Colindale, London, UK
| | - Neil Woodford
- The National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,National Infection Service, Public Health England, Colindale, London, UK
| | - A Sarah Walker
- The National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Biomedical Research Centre, Oxford, UK
| | - Julie V Robotham
- The National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.,National Infection Service, Public Health England, Colindale, London, UK
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Ray MJ, Lin MY, Weinstein RA, Trick WE. Spread of Carbapenem-Resistant Enterobacteriaceae Among Illinois Healthcare Facilities: The Role of Patient Sharing. Clin Infect Dis 2016; 63:889-93. [PMID: 27486116 DOI: 10.1093/cid/ciw461] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 06/02/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacteriaceae (CRE) spread regionally throughout healthcare facilities through patient transfer and cause difficult-to-treat infections. We developed a state-wide patient-sharing matrix and applied social network analyses to determine whether greater connectedness (centrality) to other healthcare facilities and greater patient sharing with long-term acute care hospitals (LTACHs) predicted higher facility CRE rates. METHODS We combined CRE case information from the Illinois extensively drug-resistant organism registry with measures of centrality calculated from a state-wide hospital discharge dataset to predict facility-level CRE rates, adjusting for hospital size and geographic characteristics. RESULTS Higher CRE rates were observed among facilities with greater patient sharing, as measured by degree centrality. Each additional hospital connection (unit of degree) conferred a 6% increase in CRE rate in rural facilities (relative risk [RR] = 1.056; 95% confidence interval [CI], 1.030-1.082) and a 3% increase among Chicagoland and non-Chicago urban facilities (RR = 1.027; 95% CI, 1.002-1.052 and RR = 1.025; 95% CI, 1.002-1.048, respectively). Sharing 4 or more patients with LTACHs was associated with higher CRE rates, but this association may have been due to chance (RR = 2.08; 95% CI, .85-5.08; P = .11). CONCLUSIONS Hospitals with greater connectedness to other hospitals in a statewide patient-sharing network had higher CRE burden. Centrality had a greater effect on CRE rates in rural counties, which do not have LTACHs. Social network analysis likely identifies hospitals at higher risk of CRE exposure, enabling focused clinical and public health interventions.
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Affiliation(s)
- Michael J Ray
- Division of Patient Safety and Quality, Illinois Department of Public Health
| | | | - Robert A Weinstein
- Rush University Medical Center Cook County Health and Hospitals System, Chicago, Illinois
| | - William E Trick
- Rush University Medical Center Cook County Health and Hospitals System, Chicago, Illinois
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28
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Geraci DM, Giuffrè M, Bonura C, Graziano G, Saporito L, Insinga V, Rinaudo G, Aleo A, Vecchio D, Mammina C. A Snapshot on MRSA Epidemiology in a Neonatal Intensive Care Unit Network, Palermo, Italy. Front Microbiol 2016; 7:815. [PMID: 27303395 PMCID: PMC4882316 DOI: 10.3389/fmicb.2016.00815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 05/13/2016] [Indexed: 11/23/2022] Open
Abstract
Objectives: We performed a 1-year prospective surveillance study on MRSA colonization within the five NICUs of the metropolitan area of Palermo, Italy. The purpose of the study was to assess epidemiology of MRSA in NICU from a network perspective. Methods: Transfer of patients between NICUs during 2014 was traced based on the annual hospital discharge records. In the period February 2014–January 2015, in the NICU B, at the University teaching hospital, nasal swabs from all infants were collected weekly, whereas in the other four NICUs (A, C, D, E) at 4 week-intervals of time. MRSA isolates were submitted to antibiotic susceptibility testing, SCCmec typing, PCR to detect lukS-PV and lukF-PV (lukS/F-PV) genes and the gene encoding the toxic shock syndrome toxin (TSST-1), multilocus variable number tandem repeat fingerprinting (MLVF), and multilocus sequence typing (MLST). Results: In the period under study, 587 nasal swabs were obtained from NICU B, whereas 218, 180, 157, and 95 from NICUs A, C, D, and E, respectively. Two groups of NICUs at high prevalence and low prevalence of MRSA colonization were recognized. Overall, 113 isolates of MRSA were identified from 102 infants. Six MLVF types (A–F) were detected, with type C being subdivided into five subtypes. Five sequence types (STs) were found with ST22-IVa being the most frequent type in all NICUs. All the MRSA molecular subtypes, except for ST1-IVa, were identified in NICU B. Conclusions: Our findings support the need to approach surveillance and infection control in NICU in a network perspective, prioritizing referral healthcare facilities.
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Affiliation(s)
- Daniela M Geraci
- Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro," University of Palermo Palermo, Italy
| | - Mario Giuffrè
- Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro," University of Palermo Palermo, Italy
| | - Celestino Bonura
- Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro," University of Palermo Palermo, Italy
| | - Giorgio Graziano
- Post-graduate Residency School in Hygiene and Preventive Medicine, University of Palermo Palermo, Italy
| | - Laura Saporito
- Post-graduate Residency School in Hygiene and Preventive Medicine, University of Palermo Palermo, Italy
| | - Vincenzo Insinga
- Post-graduate Residency School in Pediatrics, University of Palermo Palermo, Italy
| | - Grazia Rinaudo
- Post-graduate Residency School in Pediatrics, University of Palermo Palermo, Italy
| | - Aurora Aleo
- Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro," University of Palermo Palermo, Italy
| | - Davide Vecchio
- Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro," University of Palermo Palermo, Italy
| | - Caterina Mammina
- Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro," University of Palermo Palermo, Italy
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Not just a matter of size: a hospital-level risk factor analysis of MRSA bacteraemia in Scotland. BMC Infect Dis 2016; 16:222. [PMID: 27209082 PMCID: PMC4875632 DOI: 10.1186/s12879-016-1563-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 05/11/2016] [Indexed: 11/27/2022] Open
Abstract
Background Worldwide, there is a wealth of literature examining patient-level risk factors for methicillin-resistant Staphylococcus aureus (MRSA) bacteraemia. At the hospital-level it is generally accepted that MRSA bacteraemia is more common in larger hospitals. In Scotland, size does not fully explain all the observed variation among hospitals. The aim of this study was to identify risk factors for the presence and rate of MRSA bacteraemia cases in Scottish mainland hospitals. Specific hypotheses regarding hospital size, type and connectivity were examined. Methods Data from 198 mainland Scottish hospitals (defined as having at least one inpatient per year) were analysed for financial year 2007-08 using logistic regression (Model 1: presence/absence of MRSA bacteraemia) and Poisson regression (Model 2: rate of MRSA bacteraemia). The significance of risk factors representing various measures of hospital size, type and connectivity were investigated. Results In Scotland, size was not the only significant risk factor identified for the presence and rate of MRSA bacteraemia. The probability of a hospital having at least one case of MRSA bacteraemia increased with hospital size only if the hospital exceeded a certain level of connectivity. Higher levels of MRSA bacteraemia were associated with the large, highly connected teaching hospitals with high ratios of patients to domestic staff. Conclusions A hospital’s level of connectedness within a network may be a better measure of a hospital’s risk of MRSA bacteraemia than size. This result could be used to identify high risk hospitals which would benefit from intensified infection control measures. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1563-6) contains supplementary material, which is available to authorized users.
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30
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Giuffrè M, Geraci DM, Bonura C, Saporito L, Graziano G, Insinga V, Aleo A, Vecchio D, Mammina C. The Increasing Challenge of Multidrug-Resistant Gram-Negative Bacilli: Results of a 5-Year Active Surveillance Program in a Neonatal Intensive Care Unit. Medicine (Baltimore) 2016; 95:e3016. [PMID: 26962817 PMCID: PMC4998898 DOI: 10.1097/md.0000000000003016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Colonization and infection by multidrug-resistant gram-negative bacilli (MDR GNB) in neonatal intensive care units (NICUs) are increasingly reported.We conducted a 5-year prospective cohort surveillance study in a tertiary NICU of the hospital "Paolo Giaccone," Palermo, Italy. Our objectives were to describe incidence and trends of MDR GNB colonization and the characteristics of the most prevalent organisms and to identify the risk factors for colonization. Demographic, clinical, and microbiological data were prospectively collected. Active surveillance cultures (ASCs) were obtained weekly. Clusters of colonization by extended spectrum β-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae were analyzed by conventional and molecular epidemiological tools.During the study period, 1152 infants were enrolled in the study. Prevalences of colonization by MDR GNB, ESBL-producing GNB and multiple species/genera averaged, respectively, 28.8%, 11.7%, and 3.7%. Prevalence and incidence density of colonization by MDR GNB and ESBL-producing GNB showed an upward trend through the surveillance period. Rates of ESBL-producing E coli and K pneumoniae colonization showed wide fluctuations peaking over the last 2 years. The only independent variables associated with colonization by MDR GNB and ESBL-producing organisms and multiple colonization were, respectively, the days of NICU stay (odds ratio [OR] 1.041), the days of exposure to ampicillin-sulbactam (OR 1.040), and the days of formula feeding (OR 1.031). Most clusters of E coli and K pneumoniae colonization were associated with different lineages. Ten out of 12 clusters had an outborn infant as their index case.Our study confirms that MDR GNB are an increasing challenge to NICUs. The universal once-a-week approach allowed us to understand the epidemiology of MDR GNB, to timely detect new clones and institute contact precautions, and to assess risk factors. Collection of these data can be an important tool to optimize antimicrobials use and control the emergence and dissemination of resistances in NICU.
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Affiliation(s)
- Mario Giuffrè
- From the Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro," University of Palermo, Palermo, Italy; the Azienda Ospedaliera-Universitaria Policlinico "Paolo Giaccone" (MG, CB, VI, CM), Palermo, Italy; Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro" (DMG, AA), University of Palermo, Palermo, Italy; Post-Graduate Residency School in Hygiene and Preventive Medicine (LS, GG), University of Palermo, Palermo, Italy; Post-Graduate Residency School in Pediatrics (DV), University of Palermo, Palermo, Italy
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Population Dynamics of Patients with Bacterial Resistance in Hospital Environment. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2016; 2016:1826029. [PMID: 26904150 PMCID: PMC4745325 DOI: 10.1155/2016/1826029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 12/27/2015] [Indexed: 11/18/2022]
Abstract
During the past decades, the increase of antibiotic resistance has become a major concern worldwide. The researchers found that superbugs with new type of resistance genes (NDM-1) have two aspects of transmission characteristics; the first is that the antibiotic resistance genes can horizontally transfer among bacteria, and the other is that the superbugs can spread between humans through direct contact. Based on these two transmission mechanisms, we study the dynamics of population in hospital environment where superbugs exist. In this paper, we build three mathematic models to illustrate the dynamics of patients with bacterial resistance in hospital environment. The models are analyzed using stability theory of differential equations. Positive equilibrium points of the system are investigated and their stability analysis is carried out. Moreover, the numerical simulation of the proposed model is also performed which supports the theoretical findings.
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Abstract
A large proportion of hospital-related infections are acquired and spread due to the direct contacts between patients and healthcare workers. Accordingly, proper infection prevention measures, and especially hand hygiene, are key to limit the spread of infections in nosocomial settings. However, healthcare workers frequently experience difficulties in complying strictly to hand disinfection protocols. This study was therefore aimed at the development of a hand rub with antimicrobial activity that forms a protective film on the hand, a so-called microglove, in order to enhance hand hygiene. For this purpose, various co-polymer formulations consisting of different ratios of Polyvinylpyrrolidone (PVP) and a branched C20 derivatized maleate (M20) in combination with the known biocide benzalkonium chloride (BKC) were tested for their combined film-forming and antimicrobial activities. The results of a series of novel contamination and transmission assays show that a formulation of 80% PVP and 20% M20 co-polymer with 0.9% BKC fulfils the elementary requirements for an antimicrobial microglove.
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van Bunnik BAD, Ciccolini M, Gibbons CL, Edwards G, Fitzgerald R, McAdam PR, Ward MJ, Laurenson IF, Woolhouse MEJ. Efficient national surveillance for health-care-associated infections. BMC Public Health 2015; 15:832. [PMID: 26316148 PMCID: PMC4552460 DOI: 10.1186/s12889-015-2172-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/21/2015] [Indexed: 12/16/2022] Open
Abstract
Background Detecting novel healthcare-associated infections (HCAI) as early as possible is an important public health priority. However, there is currently no evidence base to guide the design of efficient and reliable surveillance systems. Here we address this issue in the context of a novel pathogen spreading primarily between hospitals through the movement of patients. Methods Using a mathematical modelling approach we compare the current surveillance system for a HCAI that spreads primarily between hospitals due to patient movements as it is implemented in Scotland with a gold standard to determine if the current system is maximally efficient or whether it would be beneficial to alter the number and choice of hospitals in which to concentrate surveillance effort. Results We validated our model by demonstrating that it accurately predicts the risk of meticillin-resistant Staphylococcus aureus bacteraemia cases in Scotland. Using the 29 (out of 182) sentinel hospitals that currently contribute most of the national surveillance effort results in an average detection time of 117 days. A reduction in detection time to 87 days is possible by optimal selection of 29 hospitals. Alternatively, the same detection time (117 days) can be achieved using just 22 optimally selected hospitals. Increasing the number of sentinel hospitals to 38 (teaching and general hospitals) reduces detection time by 43 days; however decreasing the number to seven sentinel hospitals (teaching hospitals) increases detection time substantially to 268 days. Conclusions Our results show that the current surveillance system as it is used in Scotland is not optimal in detecting novel pathogens when compared to a gold standard. However, efficiency gains are possible by better choice of sentinel hospitals, or by increasing the number of hospitals involved in surveillance. Similar studies could be used elsewhere to inform the design and implementation of efficient national, hospital-based surveillance systems that achieve rapid detection of novel HCAIs for minimal effort. Electronic supplementary material The online version of this article (doi:10.1186/s12889-015-2172-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B A D van Bunnik
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK.
| | - M Ciccolini
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - C L Gibbons
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK.
| | - G Edwards
- Microbiology Department, Scottish MRSA Reference Laboratory, Glasgow, UK.
| | - R Fitzgerald
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh, UK.
| | - P R McAdam
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh, UK.
| | - M J Ward
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK.
| | - I F Laurenson
- Scottish Mycobacteria Reference Laboratory, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK.
| | - M E J Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK.
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Hospital Transfer Network Structure as a Risk Factor for Clostridium difficile Infection. Infect Control Hosp Epidemiol 2015; 36:1031-7. [PMID: 26072907 DOI: 10.1017/ice.2015.130] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To determine the effect of interhospital patient sharing via transfers on the rate of Clostridium difficile infections in a hospital. DESIGN Retrospective cohort. METHODS Using data from the Healthcare Cost and Utilization Project California State Inpatient Database, 2005-2011, we identified 2,752,639 transfers. We then constructed a series of networks detailing the connections formed by hospitals. We computed 2 measures of connectivity, indegree and weighted indegree, measuring the number of hospitals from which transfers into a hospital arrive, and the total number of incoming transfers, respectively. Next, we estimated a multivariate model of C. difficile infection cases using the log-transformed network measures as well as covariates for hospital fixed effects, log median length of stay, log fraction of patients aged 65 or older, and quarter and year indicators as predictors. RESULTS We found an increase of 1 in the log indegree was associated with a 4.8% increase in incidence of C. difficile infection (95% CI, 2.3%-7.4%) and an increase of 1 in log weighted indegree was associated with a 3.3% increase in C. difficile infection incidence (1.5%-5.2%). Moreover, including measures of connectivity in our models greatly improved their fit. CONCLUSIONS Our results suggest infection control is not under the exclusive control of a given hospital but is also influenced by the connections and number of connections that hospitals have with other hospitals.
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Gayral M, Bakan B, Dalgalarrondo M, Elmorjani K, Delluc C, Brunet S, Linossier L, Morel MH, Marion D. Lipid partitioning in maize (Zea mays L.) endosperm highlights relationships among starch lipids, amylose, and vitreousness. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3551-3558. [PMID: 25794198 DOI: 10.1021/acs.jafc.5b00293] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Content and composition of maize endosperm lipids and their partition in the floury and vitreous regions were determined for a set of inbred lines. Neutral lipids, i.e., triglycerides and free fatty acids, accounted for more than 80% of endosperm lipids and are almost 2 times higher in the floury than in the vitreous regions. The composition of endosperm lipids, including their fatty acid unsaturation levels, as well as their distribution may be related to metabolic specificities of the floury and vitreous regions in carbon and nitrogen storage and to the management of stress responses during endosperm cell development. Remarkably, the highest contents of starch lipids were observed systematically within the vitreous endosperm. These high amounts of starch lipids were mainly due to lysophosphatidylcholine and were tightly linked to the highest amylose content. Consequently, the formation of amylose-lysophosphatidylcholine complexes has to be considered as an outstanding mechanism affecting endosperm vitreousness.
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Affiliation(s)
- Mathieu Gayral
- †INRA, Biopolymers, Interactions, Assemblies Research Unit, La Géraudière 44316 Nantes Cedex 3, France
| | - Bénédicte Bakan
- †INRA, Biopolymers, Interactions, Assemblies Research Unit, La Géraudière 44316 Nantes Cedex 3, France
| | - Michele Dalgalarrondo
- †INRA, Biopolymers, Interactions, Assemblies Research Unit, La Géraudière 44316 Nantes Cedex 3, France
| | - Khalil Elmorjani
- †INRA, Biopolymers, Interactions, Assemblies Research Unit, La Géraudière 44316 Nantes Cedex 3, France
| | | | - Sylvie Brunet
- §Limagrain Cereal Ingredients ZAC Les Portes de Riom, Avenue George Gershwin 63200 RIOM Cedex, France
| | - Laurent Linossier
- §Limagrain Cereal Ingredients ZAC Les Portes de Riom, Avenue George Gershwin 63200 RIOM Cedex, France
| | - Marie-Hélène Morel
- ∥INRA, Agropolymers Engineering and Emerging Technologies, 2 place Pierre Viala, 34060 Montpellier Cedex 02, France
| | - Didier Marion
- †INRA, Biopolymers, Interactions, Assemblies Research Unit, La Géraudière 44316 Nantes Cedex 3, France
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