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Kim D, Canovas-Segura B, Jimeno-Almazán A, Campos M, Juarez JM. Spatial-temporal simulation for hospital infection spread and outbreaks of Clostridioides difficile. Sci Rep 2023; 13:20022. [PMID: 37974000 PMCID: PMC10654661 DOI: 10.1038/s41598-023-47296-1] [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: 08/03/2023] [Accepted: 11/11/2023] [Indexed: 11/19/2023] Open
Abstract
Validated and curated datasets are essential for studying the spread and control of infectious diseases in hospital settings, requiring clinical information on patients' evolution and their location. The literature shows that approaches based on Artificial Intelligence (AI) in the development of clinical-support systems have benefits that are increasingly recognized. However, there is a lack of available high-volume data, necessary for trusting such AI models. One effective method in this situation involves the simulation of realistic data. Existing simulators primarily focus on implementing compartmental epidemiological models and contact networks to validate epidemiological hypotheses. Nevertheless, other practical aspects such as the hospital building distribution, shifts or safety policies on infections has received minimal attention. In this paper, we propose a novel approach for a simulator of nosocomial infection spread, combining agent-based patient description, spatial-temporal constraints of the hospital settings, and microorganism behavior driven by epidemiological models. The predictive validity of the model was analyzed considering micro and macro-face validation, parameter calibration based on literature review, model alignment, and sensitive analysis with an expert. This simulation model is useful in monitoring infections and in the decision-making process in a hospital, by helping to detect spatial-temporal patterns and predict statistical data about the disease.
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Affiliation(s)
- Denisse Kim
- Med AI Lab, University of Murcia, Campus Espinardo, 30100, Murcia, Spain.
| | | | - Amaya Jimeno-Almazán
- Internal Medicine Service, Infectious Diseases Section, Hospital Universitario Santa Lucía, Cartagena, Spain
| | - Manuel Campos
- Med AI Lab, University of Murcia, Campus Espinardo, 30100, Murcia, Spain
- Murcian Bio-Health Institute (IMIB-Arrixaca), El Palmar, 30120, Murcia, Spain
| | - Jose M Juarez
- Med AI Lab, University of Murcia, Campus Espinardo, 30100, Murcia, Spain
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Reichert E, Yaesoubi R, Rönn MM, Gift TL, Salomon JA, Grad YH. Resistance-minimising strategies for introducing a novel antibiotic for gonorrhoea treatment: a mathematical modelling study. THE LANCET. MICROBE 2023; 4:e781-e789. [PMID: 37619582 PMCID: PMC10865326 DOI: 10.1016/s2666-5247(23)00145-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/17/2023] [Accepted: 05/03/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Gonorrhoea is a highly prevalent sexually transmitted infection and an urgent public health concern because of increasing antibiotic resistance in Neisseria gonorrhoeae. Only ceftriaxone remains as the recommended treatment in the USA. With the prospect of new anti-gonococcal antibiotics being approved, we aimed to evaluate how to deploy a new drug to maximise its clinically useful lifespan. METHODS We used a compartmental model of gonorrhoea transmission in a US population of men who have sex with men (MSM) to compare strategies for introducing a new antibiotic for gonorrhoea treatment. The MSM population was stratified into three sexual activity groups (low, intermediate, and high) characterised by annual rates of partner change. The four introduction strategies tested were: (1) random 50-50 allocation, where each treatment-seeking infected individual had a 50% probability of receiving either drug A (current drug; a ceftriaxone-like antibiotic) or drug B (a new antibiotic), effective at time 0; (2) combination therapy of both the current drug and the new antibiotic; (3) reserve strategy, by which the new antibiotic was held in reserve until the current therapy reached a 5% threshold prevalence of resistance; and (4) gradual switch, or the gradual introduction of the new drug until random 50-50 allocation was reached. The primary outcome of interest was the time until 5% prevalence of resistance to each of the drugs (the new drug and the current ceftriaxone-like antibiotic); sensitivity of the primary outcome to the properties of the new antibiotic, specifically the probability of resistance emergence after treatment and the fitness costs of resistance, was explored. Secondary outcomes included the time to a 1% resistance threshold for each drug, as well as population-level prevalence, mean and range annual incidence, and the cumulative number of incident gonococcal infections. FINDINGS Under baseline model conditions, a 5% prevalence of resistance to each of drugs A and B was reached within 13·9 years with the reserve strategy, 18·2 years with the gradual switch strategy, 19·2 years with the random 50-50 allocation strategy, and 19·9 years with the combination therapy strategy. The reserve strategy was consistently inferior for mitigating antibiotic resistance under the parameter space explored and was increasingly outperformed by the other strategies as the probability of de novo resistance emergence decreased and as the fitness costs associated with resistance increased. Combination therapy tended to prolong the development of antibiotic resistance and minimise the number of annual gonococcal infections (under baseline model conditions, mean number of incident infections per year 178 641 [range 177 998-181 731] with combination therapy, 180 084 [178 011-184 405] with the reserve strategy). INTERPRETATION Our study argues for rapid introduction of new anti-gonococcal antibiotics, recognising that the feasibility of each strategy must incorporate cost, safety, and other practical concerns. The analyses should be revisited once robust estimates of key parameters-ie, the likelihood of emergence of resistance and fitness costs of resistance for the new antibiotic-are available. FUNDING US Centers for Disease Control and Prevention, National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Emily Reichert
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Reza Yaesoubi
- Department of Health Policy and Management, Yale School of Public Health, New Haven, CT, USA
| | - Minttu M Rönn
- Department of Global Health and Population, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Thomas L Gift
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joshua A Salomon
- Department of Health Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
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Reichert E, Yaesoubi R, Rönn MM, Gift TL, Salomon JA, Grad YH. Resistance-minimizing strategies for introducing a novel antibiotic for gonorrhea treatment: a mathematical modeling study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.14.23285710. [PMID: 36824857 PMCID: PMC9949214 DOI: 10.1101/2023.02.14.23285710] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Background Gonorrhea is a highly prevalent sexually transmitted infection and an urgent public health concern due to increasing antibiotic resistance. Only ceftriaxone remains as the recommended treatment in the U.S. The prospect of approval of new anti-gonococcal antibiotics raises the question of how to deploy a new drug to maximize its clinically useful lifespan. Methods We used a compartmental model of gonorrhea transmission in the U.S. population of men who have sex with men to compare strategies for introducing a new antibiotic for gonorrhea treatment. The strategies tested included holding the new antibiotic in reserve until the current therapy reached a threshold prevalence of resistance; using either drug, considering immediate and gradual introduction of the new drug; and combination therapy. The primary outcome of interest was the time until 5% prevalence of resistance to both the novel drug and to the current first-line drug (ceftriaxone). Findings The reserve strategy was consistently inferior for mitigating antibiotic resistance under the parameter space explored. The reserve strategy was increasingly outperformed by the other strategies as the probability of de novo resistance emergence decreased and as the fitness costs associated with resistance increased. Combination therapy tended to prolong the development of antibiotic resistance and minimize the number of annual gonococcal infections. Interpretation Our study argues for rapid introduction of new anti-gonococcal antibiotics, recognizing that the feasibility of each strategy must incorporate cost, safety, and other practical concerns. The analyses should be revisited once robust estimates of key parameters-likelihood of emergence of resistance and fitness costs of resistance for the new antibiotic-are available. Funding U.S. Centers for Disease Control and Prevention (CDC), National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- E Reichert
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - R Yaesoubi
- Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, USA
| | - M M Rönn
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - T L Gift
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J A Salomon
- Department of Health Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Y H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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Hou J, Long X, Wang X, Li L, Mao D, Luo Y, Ren H. Global trend of antimicrobial resistance in common bacterial pathogens in response to antibiotic consumption. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130042. [PMID: 36182890 DOI: 10.1016/j.jhazmat.2022.130042] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The emergence of antimicrobial resistance (AMR) is a growing public health threat worldwide and antibiotic consumption is being increasingly recognized as the main selective pressure driving this resistance. However, global trend in antibiotic resistance in response to antibiotic consumption is not fully understood. In this study, we collected national resistance data on specific resistant pathogens considered by the World Health Organization (WHO) as priority and antibiotic consumption data for 61 countries to assess the global trends in antibiotic resistance of those common bacterial pathogens and their association with antibiotic consumption. The low- and middle-income countries (LMICs) represented the largest hotspots of resistance, which presented relatively higher resistance rates in common bacterial pathogens but lower antibiotic consumption rates compared to high-income countries (HICs). Specifically, we developed the Normalized Antibiotic Resistance/Consumption Index (NARCI) and produced global maps of NARCI to roughly assess the appropriateness of antibiotic consumption across countries and to indicate the potentially inappropriate antibiotic consumption in LMICs compared with HICs. Additionally, we linked antibiotic consumption rates and resistance rates of target pathogens, in conjunction with NARCI and the correlation analysis between antibiotic use and resistance, to inform strategies to alleviate the threat of antibiotic resistance worldwide.
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Affiliation(s)
- Jie Hou
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Xiang Long
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Linyun Li
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China.
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China.
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
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Chen S, Li Z, Shi J, Zhou W, Zhang H, Chang H, Cao X, Gu C, Chen G, Kang Y, Chen Y, Wu C. A Nonlinear Time-Series Analysis to Identify the Thresholds in Relationships Between Antimicrobial Consumption and Resistance in a Chinese Tertiary Hospital. Infect Dis Ther 2022; 11:1019-1032. [PMID: 35290657 PMCID: PMC9124282 DOI: 10.1007/s40121-022-00608-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/10/2022] [Indexed: 01/10/2023] Open
Abstract
Introduction Balancing the benefits and risks of antimicrobials in health care requires an understanding of their effects on antimicrobial resistance at the population scale. Therefore, we aimed to investigate the association between the population antibiotics use and resistance rates and further identify their critical thresholds. Methods Data for monthly consumption of six antibiotics (daily defined doses [DDDs]/1000 inpatient-days) and the number of cases caused by five common drug-resistant bacteria (occupied bed days [OBDs]/10,000 inpatient-days) from inpatients during 2009–2020 were retrieved from the electronic prescription system at Nanjing Drum Tower Hospital, a tertiary hospital in Jiangsu Province, China. Then, a nonlinear time series analysis method, named generalized additive models (GAM), was applied to analyze the pairwise relationships and thresholds of these antibiotic consumption and resistance. Results The incidence densities of carbapenem-resistant Acinetobacter baumannii (CRAB), carbapenem-resistant Klebsiella pneumoniae (CRKP), and aminoglycoside-resistant Pseudomonas aeruginosa were all strongly synchronized with recent hospital use of carbapenems and glycopeptides. Besides, the prevalence of carbapenem-resistant Escherichia coli was also highly connected the consumption of carbapenems and fluoroquinolones. To lessen resistance, we determined a threshold for carbapenem and glycopeptide usage, where the maximum consumption should not exceed 31.042 and 25.152 DDDs per 1000 OBDs, respectively; however, the thresholds of fluoroquinolones, third-generation cephalosporin, aminoglycosides, and β-lactams have not been identified. Conclusions The inappropriate usage of carbapenems and glycopeptides was proved to drive the incidence of common drug-resistant bacteria in hospitals. Nonlinear time series analysis provided an efficient and simple way to determine the thresholds of these antibiotics, which could provide population-specific quantitative targets for antibiotic stewardship.
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Affiliation(s)
- Shixing Chen
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Zepeng Li
- Business School, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Jiping Shi
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Wanqing Zhou
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Haixia Zhang
- Department of Pharmacy, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, People's Republic of China
| | - Haiyan Chang
- Department of Infectious Diseases, The First Affiliated Hospital of Xinxiang Medical College, Weihui, Henan, People's Republic of China
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Changgui Gu
- Business School, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Guangmei Chen
- Department of Infectious Diseases, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, People's Republic of China
| | - Yi Kang
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, Jiangsu, People's Republic of China.
| | - Chao Wu
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210008, Jiangsu, People's Republic of China.
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Gowler CD, Slayton RB, Reddy SC, O’Hagan JJ. Improving mathematical modeling of interventions to prevent healthcare-associated infections by interrupting transmission or pathogens: How common modeling assumptions about colonized individuals impact intervention effectiveness estimates. PLoS One 2022; 17:e0264344. [PMID: 35226689 PMCID: PMC8884501 DOI: 10.1371/journal.pone.0264344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 02/08/2022] [Indexed: 12/03/2022] Open
Abstract
Mathematical models are used to gauge the impact of interventions for healthcare-associated infections. As with any analytic method, such models require many assumptions. Two common assumptions are that asymptomatically colonized individuals are more likely to be hospitalized and that they spend longer in the hospital per admission because of their colonization status. These assumptions have no biological basis and could impact the estimated effects of interventions in unintended ways. Therefore, we developed a model of methicillin-resistant Staphylococcus aureus transmission to explicitly evaluate the impact of these assumptions. We found that assuming that asymptomatically colonized individuals were more likely to be admitted to the hospital or spend longer in the hospital than uncolonized individuals biased results compared to a more realistic model that did not make either assumption. Results were heavily biased when estimating the impact of an intervention that directly reduced transmission in a hospital. In contrast, results were moderately biased when estimating the impact of an intervention that decolonized hospital patients. Our findings can inform choices modelers face when constructing models of healthcare-associated infection interventions and thereby improve their validity.
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Affiliation(s)
- Camden D. Gowler
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rachel B. Slayton
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sujan C. Reddy
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Justin J. O’Hagan
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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Gruenberg K, Abdoler E, O'Brien BC, Schwartz BS, MacDougall C. How do pharmacists select antimicrobials? A model of pharmacists' therapeutic reasoning processes. JOURNAL OF THE AMERICAN COLLEGE OF CLINICAL PHARMACY 2021. [DOI: 10.1002/jac5.1580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Katherine Gruenberg
- Department of Clinical Pharmacy University of California San Francisco San Francisco California USA
| | - Emily Abdoler
- Department of Medicine University of Michigan Ann Arbor Michigan USA
| | - Bridget C. O'Brien
- Department of Medicine University of California San Francisco San Francisco California USA
| | - Brian S. Schwartz
- Department of Medicine University of California San Francisco San Francisco California USA
| | - Conan MacDougall
- Department of Clinical Pharmacy University of California San Francisco San Francisco California USA
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Andersson DI, Balaban NQ, Baquero F, Courvalin P, Glaser P, Gophna U, Kishony R, Molin S, Tønjum T. Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiol Rev 2020; 44:171-188. [PMID: 31981358 DOI: 10.1093/femsre/fuaa001] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/24/2020] [Indexed: 02/06/2023] Open
Abstract
Antibiotic resistance is one of the major challenges facing modern medicine worldwide. The past few decades have witnessed rapid progress in our understanding of the multiple factors that affect the emergence and spread of antibiotic resistance at the population level and the level of the individual patient. However, the process of translating this progress into health policy and clinical practice has been slow. Here, we attempt to consolidate current knowledge about the evolution and ecology of antibiotic resistance into a roadmap for future research as well as clinical and environmental control of antibiotic resistance. At the population level, we examine emergence, transmission and dissemination of antibiotic resistance, and at the patient level, we examine adaptation involving bacterial physiology and host resilience. Finally, we describe new approaches and technologies for improving diagnosis and treatment and minimizing the spread of resistance.
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Affiliation(s)
- Dan I Andersson
- Department of Medical Biochemistry and Microbiology, University of Uppsala, BMC, Husargatan 3, 75237, Uppsala, Sweden
| | - Nathalie Q Balaban
- The Racah Institute of Physics, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Jerusalem, Israel
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal Health Research Institute, Ctra. Colmenar Viejo Km 9,100 28034 - Madrid, Madrid, Spain
| | - Patrice Courvalin
- French National Reference Center for Antibiotics, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, Paris, France
| | - Uri Gophna
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, 121 Jack Green building, Tel-Aviv University, Ramat-Aviv, 6997801, Tel Aviv, Israel
| | - Roy Kishony
- Faculty of Biology, The Technion, Technion City, Haifa 3200003, Haifa, Israel
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220 2800 Kgs.Lyngby, Lyngby, Denmark
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, OUS HF Rikshospitalet Postboks 4950 Nydalen 0424 Oslo, Oslo, Norway.,Oslo University Hospital, P. O. Box 4950 Nydalen N-0424 Oslo, Oslo, Norway
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Jeffrey B, Aanensen DM, Croucher NJ, Bhatt S. Predicting the future distribution of antibiotic resistance using time series forecasting and geospatial modelling. Wellcome Open Res 2020. [DOI: 10.12688/wellcomeopenres.16153.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Increasing antibiotic resistance in a location may be mitigated by changes in treatment policy, or interventions to limit transmission of resistant bacteria. Therefore, accurate forecasting of the distribution of antibiotic resistance could be advantageous. Two previously published studies addressed this, but neither study compared alternative forecasting algorithms or considered spatial patterns of resistance spread. Methods: We analysed data describing the annual prevalence of antibiotic resistance per country in Europe from 2012 – 2016, and the quarterly prevalence of antibiotic resistance per clinical commissioning group in England from 2015 – 2018. We combined these with data on rates of possible covariates of resistance. These data were used to compare the previously published forecasting models, with other commonly used forecasting models, including one geospatial model. Covariates were incorporated into the geospatial model to assess their relationship with antibiotic resistance. Results: For the European data, which was recorded on a coarse spatiotemporal scale, a naïve forecasting model was consistently the most accurate of any of the forecasting models tested. The geospatial model did not improve on this accuracy. However, it did provide some evidence that antibiotic consumption can partially explain the distribution of resistance. The English data were aggregated at a finer scale, and expected-trend-seasonal (ETS) forecasts were the most accurate. The geospatial model did not significantly improve upon the median accuracy of the ETS model, but it appeared to be less sensitive to noise in the data, and provided evidence that rates of antibiotic prescription and bacteraemia are correlated with resistance. Conclusion: Annual, national-level surveillance data appears to be insufficient for fitting accurate antibiotic resistance forecasting models, but there is evidence that data collected at a finer spatiotemporal scale could be used to improve forecast accuracy. Additionally, incorporating antibiotic prescription or consumption data into the model could improve the predictive accuracy.
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Tetteh JNA, Matthäus F, Hernandez-Vargas EA. A survey of within-host and between-hosts modelling for antibiotic resistance. Biosystems 2020; 196:104182. [PMID: 32525023 DOI: 10.1016/j.biosystems.2020.104182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance is a global public health problem which has the attention of many stakeholders including clinicians, the pharmaceutical industry, researchers and policy makers. Despite the existence of many studies, control of resistance transmission has become a rather daunting task as the mechanisms underlying resistance evolution and development are not fully known. Here, we discuss the mechanisms underlying antibiotic resistance development, explore some treatment strategies used in the fight against antibiotic resistance and consider recent findings on collateral susceptibilities amongst antibiotic classes. Mathematical models have proved valuable for unravelling complex mechanisms in biology and such models have been used in the quest of understanding the development and spread of antibiotic resistance. While assessing the importance of such mathematical models, previous systematic reviews were interested in investigating whether these models follow good modelling practice. We focus on theoretical approaches used for resistance modelling considering both within and between host models as well as some pharmacodynamic and pharmakokinetic approaches and further examine the interaction between drugs and host immune response during treatment with antibiotics. Finally, we provide an outlook for future research aimed at modelling approaches for combating antibiotic resistance.
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Affiliation(s)
- Josephine N A Tetteh
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Strasse 1, 60438, Frankfurt am Main, Germany; Institut für Mathematik, Goethe-Universität, Frankfurt am Main, Germany
| | - Franziska Matthäus
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Strasse 1, 60438, Frankfurt am Main, Germany; Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | - Esteban A Hernandez-Vargas
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Strasse 1, 60438, Frankfurt am Main, Germany; Instituto de Matemáticas, UNAM, Unidad Juriquilla, Blvd. Juriquilla 3001, Juriquilla, Queretaro, 76230, Mexico.
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Effects of the proportion of high-risk patients and control strategies on the prevalence of methicillin-resistant Staphylococcus aureus in an intensive care unit. BMC Infect Dis 2019; 19:1026. [PMID: 31795957 PMCID: PMC6889565 DOI: 10.1186/s12879-019-4632-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/11/2019] [Indexed: 11/26/2022] Open
Abstract
Background The presence of nosocomial pathogens in many intensive care units poses a threat to patients and public health worldwide. Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen endemic in many hospital settings. Patients who are colonized with MRSA may develop an infection that can complicate their prior illness. Methods A mathematical model to describe transmission dynamics of MRSA among high-risk and low-risk patients in an intensive care unit (ICU) via hands of health care workers is developed. We aim to explore the effects of the proportion of high-risk patients, the admission proportions of colonized and infected patients, the probability of developing an MRSA infection, and control strategies on MRSA prevalence among patients. Results The increasing proportion of colonized and infected patients at admission, along with the higher proportion of high-risk patients in an ICU, may significantly increase MRSA prevalence. In addition, the prevalence becomes higher if patients in the high-risk group are more likely to develop an MRSA infection. Our results also suggest that additional infection prevention and control measures targeting high-risk patients may considerably help reduce MRSA prevalence as compared to those targeting low-risk patients. Conclusions The proportion of high-risk patients and the proportion of colonized and infected patients in the high-risk group at admission may play an important role on MRSA prevalence. Control strategies targeting high-risk patients may help reduce MRSA prevalence.
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López-Lozano JM, Lawes T, Nebot C, Beyaert A, Bertrand X, Hocquet D, Aldeyab M, Scott M, Conlon-Bingham G, Farren D, Kardos G, Fésűs A, Rodríguez-Baño J, Retamar P, Gonzalo-Jiménez N, Gould IM. A nonlinear time-series analysis approach to identify thresholds in associations between population antibiotic use and rates of resistance. Nat Microbiol 2019; 4:1160-1172. [PMID: 30962570 DOI: 10.1038/s41564-019-0410-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 02/13/2019] [Indexed: 11/09/2022]
Abstract
Balancing access to antibiotics with the control of antibiotic resistance is a global public health priority. At present, antibiotic stewardship is informed by a 'use it and lose it' principle, in which antibiotic use by the population is linearly related to resistance rates. However, theoretical and mathematical models suggest that use-resistance relationships are nonlinear. One explanation for this is that resistance genes are commonly associated with 'fitness costs' that impair the replication or transmissibility of the pathogen. Therefore, resistant genes and pathogens may only gain a survival advantage where antibiotic selection pressures exceed critical thresholds. These thresholds may provide quantitative targets for stewardship-optimizing the control of resistance while avoiding over-restriction of antibiotics. Here, we evaluated the generalizability of a nonlinear time-series analysis approach for identifying thresholds using historical prescribing and microbiological data from five populations in Europe. We identified minimum thresholds in temporal relationships between the use of selected antibiotics and incidence rates of carbapenem-resistant Acinetobacter baumannii (Hungary), extended-spectrum β-lactamase-producing Escherichia coli (Spain), cefepime-resistant E. coli (Spain), gentamicin-resistant Pseudomonas aeruginosa (France) and methicillin-resistant Staphylococcus aureus (Northern Ireland) in different epidemiological phases. Using routinely generated data, our approach can identify context-specific quantitative targets for rationalizing population antibiotic use and controlling resistance. Prospective intervention studies that restrict antibiotic consumption are needed to validate these thresholds.
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Affiliation(s)
| | - Timothy Lawes
- The Wellcome Trust Liverpool-Glasgow Centre for Global Health Research, Liverpool, UK.
| | - César Nebot
- Centro Universitario de la Defensa de San Javier, Murcia, Spain
| | - Arielle Beyaert
- Departamento de Métodos Cuantitativos para la Economía y la Empresa, University of Murcia, Murcia, Spain
| | - Xavier Bertrand
- Laboratoire Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France.,Centre Hospitalier Régional Universitaire de Besançon, Besançon, France
| | - Didier Hocquet
- Laboratoire Chrono-environnement, Université de Bourgogne-Franche-Comté, Besançon, France.,Centre Hospitalier Régional Universitaire de Besançon, Besançon, France
| | - Mamoon Aldeyab
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Michael Scott
- Pharmacy Department, Northern Health and Social Care Trust and Regional Medicines Optimisation Innovation Centre, Antrim, UK
| | - Geraldine Conlon-Bingham
- Pharmacy Department, Northern Health and Social Care Trust and Regional Medicines Optimisation Innovation Centre, Antrim, UK
| | - David Farren
- Department of Medical Microbiology, Antrim Area Hospital, Antrim, UK
| | - Gábor Kardos
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Adina Fésűs
- Clinical Pharmacy, University of Debrecen, Debrecen, Hungary
| | - Jesús Rodríguez-Baño
- Infectious Diseases and Clinical Microbiology Unit, Hospital Universitario Virgen Macarena, Seville, Spain.,Department of Medicine, Instituto de Biomedicina de Sevilla, University of Sevilla, Seville, Spain
| | - Pilar Retamar
- Infectious Diseases and Clinical Microbiology Unit, Hospital Universitario Virgen Macarena, Seville, Spain.,Department of Medicine, Instituto de Biomedicina de Sevilla, University of Sevilla, Seville, Spain
| | | | - Ian M Gould
- Medical Microbiology Department, Aberdeen Royal Infirmary, Aberdeen, UK
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Campos M, Capilla R, Naya F, Futami R, Coque T, Moya A, Fernandez-Lanza V, Cantón R, Sempere JM, Llorens C, Baquero F. Simulating Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model. mBio 2019; 10:mBio.02460-18. [PMID: 30696743 PMCID: PMC6355984 DOI: 10.1128/mbio.02460-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Membrane computing is a bio-inspired computing paradigm whose devices are the so-called membrane systems or P systems. The P system designed in this work reproduces complex biological landscapes in the computer world. It uses nested "membrane-surrounded entities" able to divide, propagate, and die; to be transferred into other membranes; to exchange informative material according to flexible rules; and to mutate and be selected by external agents. This allows the exploration of hierarchical interactive dynamics resulting from the probabilistic interaction of genes (phenotypes), clones, species, hosts, environments, and antibiotic challenges. Our model facilitates analysis of several aspects of the rules that govern the multilevel evolutionary biology of antibiotic resistance. We examined a number of selected landscapes where we predict the effects of different rates of patient flow from hospital to the community and vice versa, the cross-transmission rates between patients with bacterial propagules of different sizes, the proportion of patients treated with antibiotics, and the antibiotics and dosing found in the opening spaces in the microbiota where resistant phenotypes multiply. We also evaluated the selective strengths of some drugs and the influence of the time 0 resistance composition of the species and bacterial clones in the evolution of resistance phenotypes. In summary, we provide case studies analyzing the hierarchical dynamics of antibiotic resistance using a novel computing model with reciprocity within and between levels of biological organization, a type of approach that may be expanded in the multilevel analysis of complex microbial landscapes.IMPORTANCE The work that we present here represents the culmination of many years of investigation in looking for a suitable methodology to simulate the multihierarchical processes involved in antibiotic resistance. Everything started with our early appreciation of the different independent but embedded biological units that shape the biology, ecology, and evolution of antibiotic-resistant microorganisms. Genes, plasmids carrying these genes, cells hosting plasmids, populations of cells, microbial communities, and host's populations constitute a complex system where changes in one component might influence the other ones. How would it be possible to simulate such a complexity of antibiotic resistance as it occurs in the real world? Can the process be predicted, at least at the local level? A few years ago, and because of their structural resemblance to biological systems, we realized that membrane computing procedures could provide a suitable frame to approach these questions. Our manuscript describes the first application of this modeling methodology to the field of antibiotic resistance and offers a bunch of examples-just a limited number of them in comparison with the possible ones to illustrate its unprecedented explanatory power.
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Affiliation(s)
- Marcelino Campos
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Department of Information Systems and Computation (DSIC), Universitat Politècnica de València, Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | | | | | | | - Teresa Coque
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), Superior Council of Scientific Research (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Andrés Moya
- Integrative Systems Biology Institute, University of Valencia and Spanish Research Council (CSIC), Paterna, Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research in the Valencian Community (FISABIO), Valencia, Spain
| | - Val Fernandez-Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Bioinformatics Support Unit, IRYCIS, Madrid, Spain
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), Superior Council of Scientific Research (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - José M Sempere
- Department of Information Systems and Computation (DSIC), Universitat Politècnica de València, Valencia, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, Spain
- Antibiotic Resistance and Bacterial Virulence Unit (HRYC-CSIC), Superior Council of Scientific Research (CSIC), Madrid, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
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Rubio A, Pucci MJ, Jain A. Characterization of SPR994, an Orally Available Carbapenem, with Activity Comparable to Intravenously Administered Carbapenems. ACS Infect Dis 2018; 4:1436-1438. [PMID: 30118209 DOI: 10.1021/acsinfecdis.8b00188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Carbapenems are potent antibacterials with broad-spectrum activity. However, poor oral absorption generally confines this important drug class to in-hospital use by intravenous (IV) administration. The continued rise in drug resistant pathogens creates a need for alternative oral therapies with broad-spectrum activity. SPR994 is a novel formulation of the orally bioavailable pivoxil prodrug of SPR859 (tebipenem) and is being developed as the first oral carbapenem for treatment of complicated urinary tract infections (cUTIs) in adults. Herein, we describe characteristics beneficial to oral administration and compare the in vitro and in vivo activity of SPR859 or SPR994 with IV carbapenems.
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Affiliation(s)
- Aileen Rubio
- Spero Therapeutics, 675 Massachusetts Avenue, 14th Floor, Cambridge, Massachusetts 02139, United States
| | - Michael J. Pucci
- Spero Therapeutics, 675 Massachusetts Avenue, 14th Floor, Cambridge, Massachusetts 02139, United States
| | - Akash Jain
- Spero Therapeutics, 675 Massachusetts Avenue, 14th Floor, Cambridge, Massachusetts 02139, United States
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Birkegård AC, Halasa T, Toft N, Folkesson A, Græsbøll K. Send more data: a systematic review of mathematical models of antimicrobial resistance. Antimicrob Resist Infect Control 2018; 7:117. [PMID: 30288257 PMCID: PMC6162961 DOI: 10.1186/s13756-018-0406-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/13/2018] [Indexed: 01/23/2023] Open
Abstract
Background Antimicrobial resistance is a global health problem that demands all possible means to control it. Mathematical modelling is a valuable tool for understanding the mechanisms of AMR development and spread, and can help us to investigate and propose novel control strategies. However, it is of vital importance that mathematical models have a broad utility, which can be assured if good modelling practice is followed. Objective The objective of this study was to provide a comprehensive systematic review of published models of AMR development and spread. Furthermore, the study aimed to identify gaps in the knowledge required to develop useful models. Methods The review comprised a comprehensive literature search with 38 selected studies. Information was extracted from the selected papers using an adaptation of previously published frameworks, and was evaluated using the TRACE good modelling practice guidelines. Results None of the selected papers fulfilled the TRACE guidelines. We recommend that future mathematical models should: a) model the biological processes mechanistically, b) incorporate uncertainty and variability in the system using stochastic modelling, c) include a sensitivity analysis and model external and internal validation. Conclusion Many mathematical models of AMR development and spread exist. There is still a lack of knowledge about antimicrobial resistance, which restricts the development of useful mathematical models.
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Affiliation(s)
- Anna Camilla Birkegård
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Asmussens Allé Building 303B, 2800 Kgs. Lyngby, Denmark
| | - Tariq Halasa
- Division of Diagnostics & Scientific Advice, Technical University of Denmark, Kemitorvet Building 204, 2800 Kgs. Lyngby, Denmark
| | - Nils Toft
- Division of Diagnostics & Scientific Advice, Technical University of Denmark, Kemitorvet Building 204, 2800 Kgs. Lyngby, Denmark
| | - Anders Folkesson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kemitorvet Building 204, 2800 Kgs. Lyngby, Denmark
| | - Kaare Græsbøll
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Asmussens Allé Building 303B, 2800 Kgs. Lyngby, Denmark
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Application of dynamic modelling techniques to the problem of antibacterial use and resistance: a scoping review. Epidemiol Infect 2018; 146:2014-2027. [PMID: 30062979 DOI: 10.1017/s0950268818002091] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Selective pressure exerted by the widespread use of antibacterial drugs is accelerating the development of resistant bacterial populations. The purpose of this scoping review was to summarise the range of studies that use dynamic models to analyse the problem of bacterial resistance in relation to antibacterial use in human and animal populations. A comprehensive search of the peer-reviewed literature was performed and non-duplicate articles (n = 1486) were screened in several stages. Charting questions were used to extract information from the articles included in the final subset (n = 81). Most studies (86%) represent the system of interest with an aggregate model; individual-based models are constructed in only seven articles. There are few examples of inter-host models outside of human healthcare (41%) and community settings (38%). Resistance is modelled for a non-specific bacterial organism and/or antibiotic in 40% and 74% of the included articles, respectively. Interventions with implications for antibacterial use were investigated in 67 articles and included changes to total antibiotic consumption, strategies for drug management and shifts in category/class use. The quality of documentation related to model assumptions and uncertainty varies considerably across this subset of articles. There is substantial room to improve the transparency of reporting in the antibacterial resistance modelling literature as is recommended by best practice guidelines.
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17
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Caudill L, Lawson B. A unified inter-host and in-host model of antibiotic resistance and infection spread in a hospital ward. J Theor Biol 2017; 421:112-126. [PMID: 28365293 DOI: 10.1016/j.jtbi.2017.03.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/14/2017] [Accepted: 03/25/2017] [Indexed: 11/24/2022]
Abstract
As the battle continues against hospital-acquired infections and the concurrent rise in antibiotic resistance among many of the major causative pathogens, there is a dire need to conduct controlled experiments, in order to compare proposed control strategies. However, cost, time, and ethical considerations make this evaluation strategy either impractical or impossible to implement with living patients. This paper presents a multi-scale model that offers promise as the basis for a tool to simulate these (and other) controlled experiments. This is a "unified" model in two important ways: (i) It combines inter-host and in-host dynamics into a single model, and (ii) it links two very different modeling approaches - agent-based modeling and differential equations - into a single model. The potential of this model as an instrument to combat antibiotic resistance in hospitals is demonstrated with numerical examples.
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Affiliation(s)
- Lester Caudill
- Department of Mathematics and Computer Science, University of Richmond, Virginia 23173 USA.
| | - Barry Lawson
- Department of Mathematics and Computer Science, University of Richmond, Virginia 23173 USA
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18
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Hughes J, Huo X, Falk L, Hurford A, Lan K, Coburn B, Morris A, Wu J. Benefits and unintended consequences of antimicrobial de-escalation: Implications for stewardship programs. PLoS One 2017; 12:e0171218. [PMID: 28182774 PMCID: PMC5300270 DOI: 10.1371/journal.pone.0171218] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 01/18/2017] [Indexed: 12/19/2022] Open
Abstract
Sequential antimicrobial de-escalation aims to minimize resistance to high-value broad-spectrum empiric antimicrobials by switching to alternative drugs when testing confirms susceptibility. Though widely practiced, the effects de-escalation are not well understood. Definitions of interventions and outcomes differ among studies. We use mathematical models of the transmission and evolution of Pseudomonas aeruginosa in an intensive care unit to assess the effect of de-escalation on a broad range of outcomes, and clarify expectations. In these models, de-escalation reduces the use of high-value drugs and preserves the effectiveness of empiric therapy, while also selecting for multidrug-resistant strains and leaving patients vulnerable to colonization and superinfection. The net effect of de-escalation in our models is to increase infection prevalence while also increasing the probability of effective treatment. Changes in mortality are small, and can be either positive or negative. The clinical significance of small changes in outcomes such as infection prevalence and death may exceed more easily detectable changes in drug use and resistance. Integrating harms and benefits into ranked outcomes for each patient may provide a way forward in the analysis of these tradeoffs. Our models provide a conceptual framework for the collection and interpretation of evidence needed to inform antimicrobial stewardship.
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Affiliation(s)
- Josie Hughes
- Centre for Disease Modelling, York University, Toronto, Ontario, Canada
| | - Xi Huo
- Centre for Disease Modelling, York University, Toronto, Ontario, Canada
- Department of Mathematics, Ryerson University, Toronto, Ontario, Canada
| | - Lindsey Falk
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Amy Hurford
- Department of Biology and Department of Mathematics and Statistics, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Kunquan Lan
- Department of Mathematics, Ryerson University, Toronto, Ontario, Canada
| | - Bryan Coburn
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Medicine, Sinai Health System & University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Morris
- Department of Medicine, Sinai Health System & University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jianhong Wu
- Centre for Disease Modelling, York University, Toronto, Ontario, Canada
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Zhao B, Zhang X. Mathematical analysis of multi-antibiotic resistance. Int J Cardiol 2016; 219:33-7. [PMID: 27262230 DOI: 10.1016/j.ijcard.2016.05.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Multi-antibiotic resistance in bacterial infections is a growing threat to public health. Some experiments were carried out to study the multi-antibiotic resistance. METHODS The changes of the multi-antibiotic resistance with time were achieved by numerical simulations and the mathematical models, with the calculated temperature field, velocity field, and the antibiotic concentration field. RESULTS The computed results and experimental results are compared. CONCLUSIONS Both numerical simulations and the analytic models suggest that minor low concentrations of antibiotics could induce antibiotic resistance in bacteria.
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Affiliation(s)
- Bin Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China; College of Science, Northwest A&F University, Yangling, Shaanxi, China.
| | - Xiaoying Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
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Chaudhry LA, Al-Tawfiq JA, Zamzami MM, Al-Ghamdi SA, Robert AA. Antimicrobial susceptibility patterns: a three-year surveillance study in a rehabilitation setting. Pan Afr Med J 2016; 23:214. [PMID: 28210371 PMCID: PMC5299385 DOI: 10.11604/pamj.2016.23.214.8474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 04/03/2016] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION To analyze the susceptibility patterns in a rehabilitation center. METHODS This retrospective observational study was conducted between January 2011 and to January 2013 at Sultan Bin Abdulaziz Humanitarian City (SBAHC), Riyadh, Kingdom of Saudi Arabia. Number of the patients, specimen type, pathogen detected and antibiogram were entered in database for analysis using Inter System Track care software. RESULTS A total of 4525 isolates were available from 5148 patients. Most (74%) of the isolates were from urine samples and were due to Eschericia coli (49.8%), Enterococcus faecalis (15%) and (Proteous mirabilis(9.49%). Of all the isolates, Eschericia coli was the commonest (49.8%) Gram negative organism, while(Stahylococcus aureus was the commonest (51%) among Gram positive organisms. The most effective antibiotics against Pseudomonas aeroginosa were ciprofloxacin and gentamicin. Meropenem shows excellent activity against Gram negative bacteria. Methicillin resistant Staphylococcus aureus (MRSA) was susceptible to Vancomycin and Rifampicin in 97% and 85% cases. CONCLUSION A high incidence of urinary tract infections caused by Eschericia coli, Enterococcus faecalis and Proteous mirabilis was reported. Staphylococcus aureus was the commonest pathogen isolated from infected bed sores.
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Affiliation(s)
- Liaqat Ali Chaudhry
- Department of Internal Medicine, Pulmonary Division, Sultan Bin Abdulaziz Humanitarian City, Riyadh, Kingdom Saudi Arabia
| | - Jaffar Ali Al-Tawfiq
- Speciality Internal Medicine, John Hopkins Aramco Healthcare, Dhahran, Kingdom Saudi Arabia
| | - Marwan Mohammed Zamzami
- Department of Orthopedic Surgery, College of Medicine, King Saud University, Riyadh, Kingdom Saudi Arabia
| | - Saeed Abdullah Al-Ghamdi
- Department of Laboratory Services, Sultan Bin Abdulaziz Humanitarian City, Riyadh, Kingdom Saudi Arabia
| | - Asirvatham Alwin Robert
- Department of Endocrinology and Diabetes, Diabetes Treatment Center, Prince Sultan Military Medical City, Riyadh, Kingdom Saudi Arabia
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Mathematical modelling of bacterial resistance to multiple antibiotics and immune system response. SPRINGERPLUS 2016; 5:408. [PMID: 27069828 PMCID: PMC4820433 DOI: 10.1186/s40064-016-2017-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/16/2016] [Indexed: 12/02/2022]
Abstract
Resistance of developed bacteria to antibiotic treatment is a very important issue, because introduction of any new antibiotic is after a little while followed by the formation of resistant bacterial isolates in the clinic. The significant increase in clinical resistance to antibiotics is a troubling situation especially in nosocomial infections, where already defenseless patients can be unsuccessful to respond to treatment, causing even greater health issue. Nosocomial infections can be identified as those happening within 2 days of hospital acceptance, 3 days of discharge or 1 month of an operation. They influence 1 out of 10 patients admitted to hospital. Annually, this outcomes in 5000 deaths only in UK with a cost to the National Health Service of a billion pounds. Despite these problems, antibiotic therapy is still the most common method used to treat bacterial infections. On the other hand, it is often mentioned that immune system plays a major role in the progress of infections. In this context, we proposed a mathematical model defining population dynamics of both the specific immune cells produced according to the properties of bacteria by host and the bacteria exposed to multiple antibiotics synchronically, presuming that resistance is gained through mutations due to exposure to antibiotic. Qualitative analysis found out infection-free equilibrium point and other equilibrium points where resistant bacteria and immune system cells exist, only resistant bacteria exists and sensitive bacteria, resistant bacteria and immune system cells exist. As a result of this analysis, our model highlights the fact that when an individual’s immune system weakens, he/she suffers more from the bacterial infections which are believed to have been confined or terminated. Also, these results was supported by numerical simulations.
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Arepeva M, Kolbin A, Kurylev A, Balykina J, Sidorenko S. What should be considered if you decide to build your own mathematical model for predicting the development of bacterial resistance? Recommendations based on a systematic review of the literature. Front Microbiol 2015; 6:352. [PMID: 25972847 PMCID: PMC4413671 DOI: 10.3389/fmicb.2015.00352] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/08/2015] [Indexed: 11/17/2022] Open
Abstract
Acquired bacterial resistance is one of the causes of mortality and morbidity from infectious diseases. Mathematical modeling allows us to predict the spread of resistance and to some extent to control its dynamics. The purpose of this review was to examine existing mathematical models in order to understand the pros and cons of currently used approaches and to build our own model. During the analysis, seven articles on mathematical approaches to studying resistance that satisfied the inclusion/exclusion criteria were selected. All models were classified according to the approach used to study resistance in the presence of an antibiotic and were analyzed in terms of our research. Some models require modifications due to the specifics of the research. The plan for further work on model building is as follows: modify some models, according to our research, check all obtained models against our data, and select the optimal model or models with the best quality of prediction. After that we would be able to build a model for the development of resistance using the obtained results.
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Affiliation(s)
- Maria Arepeva
- Faculty of Applied Mathematics and Control Processes, St. Petersburg State University St. Petersburg, Russia
| | - Alexey Kolbin
- Faculty of Applied Mathematics and Control Processes, St. Petersburg State University St. Petersburg, Russia ; Faculty of Medicine, First Pavlov State Medical University of St. Petersburg St. Petersburg, Russia
| | - Alexey Kurylev
- Faculty of Medicine, First Pavlov State Medical University of St. Petersburg St. Petersburg, Russia
| | - Julia Balykina
- Faculty of Applied Mathematics and Control Processes, St. Petersburg State University St. Petersburg, Russia
| | - Sergey Sidorenko
- Department of Molecular Microbiology and Epidemiology, Scientific Research Institute of Childhood Infections St. Petersburg, Russia ; Department of Medical Microbiology, North-Western State Medical University named after I.I. Mechnikov St. Petersburg, Russia
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McGowan JE. Antimicrobial Stewardship—the State of the Art in 2011 Focus on Outcome and Methods. Infect Control Hosp Epidemiol 2015; 33:331-7. [DOI: 10.1086/664755] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Antimicrobial stewardship programs attempt to optimize prescribing of these drugs to benefit both current and future patients. Recent regulatory and other incentives have led to widespread adoption of such programs. Measurements of the success of these programs have focused primarily on process measures. However, evaluation of outcome measures will be needed to ensure sustainability of these efforts. Outcome efforts to date provide some evidence for improved care of individual patients, some evidence for minimizing emergence of resistance, and ample evidence for cost reduction. Attention to evaluation methods must be increased to provide convincing evidence for the continuation of such programs.
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Levin BR, Baquero F, Johnsen PJ. A model-guided analysis and perspective on the evolution and epidemiology of antibiotic resistance and its future. Curr Opin Microbiol 2014; 19:83-89. [PMID: 25016172 DOI: 10.1016/j.mib.2014.06.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/11/2014] [Accepted: 06/11/2014] [Indexed: 01/06/2023]
Abstract
A simple epidemiological model is used as a framework to explore the potential efficacy of measures to control antibiotic resistance in community-based self-limiting human infections. The analysis of the properties of this model predict that resistance can be maintained at manageable levels if: first, the rates at which specific antibiotics are used declines with the frequency of resistance to these drugs; second, resistance rarely emerges during therapy; and third, external sources rarely contribute to the entry of resistant bacteria into the community. We discuss the feasibility and limitations of these measures to control the rates of antibiotic resistance and the potential of advances in diagnostic procedures to facilitate this endeavor.
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Affiliation(s)
- Bruce R Levin
- Department of Biology Emory University, Atlanta, GA, USA.
| | - Fernando Baquero
- Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Pål J Johnsen
- Department of Pharmacy, UiT, The Arctic University, Tromsø, Norway
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25
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Epidemiological interpretation of studies examining the effect of antibiotic usage on resistance. Clin Microbiol Rev 2013; 26:289-307. [PMID: 23554418 DOI: 10.1128/cmr.00001-13] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bacterial resistance to antibiotics is a growing clinical problem and public health threat. Antibiotic use is a known risk factor for the emergence of antibiotic resistance, but demonstrating the causal link between antibiotic use and resistance is challenging. This review describes different study designs for assessing the association between antibiotic use and resistance and discusses strengths and limitations of each. Approaches to measuring antibiotic use and antibiotic resistance are presented. Important methodological issues such as confounding, establishing temporality, and control group selection are examined.
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Spicknall IH, Foxman B, Marrs CF, Eisenberg JNS. A modeling framework for the evolution and spread of antibiotic resistance: literature review and model categorization. Am J Epidemiol 2013; 178:508-20. [PMID: 23660797 PMCID: PMC3736756 DOI: 10.1093/aje/kwt017] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antibiotic-resistant infections complicate treatment and increase morbidity and mortality. Mathematical modeling has played an integral role in improving our understanding of antibiotic resistance. In these models, parameter sensitivity is often assessed, while model structure sensitivity is not. To examine the implications of this, we first reviewed the literature on antibiotic-resistance modeling published between 1993 and 2011. We then classified each article's model structure into one or more of 6 categories based on the assumptions made in those articles regarding within-host and population-level competition between antibiotic-sensitive and antibiotic-resistant strains. Each model category has different dynamic implications with respect to how antibiotic use affects resistance prevalence, and therefore each may produce different conclusions about optimal treatment protocols that minimize resistance. Thus, even if all parameter values are correctly estimated, inferences may be incorrect because of the incorrect selection of model structure. Our framework provides insight into model selection.
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Affiliation(s)
- Ian H Spicknall
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
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Orsi GB, Falcone M, Venditti M. Surveillance and management of multidrug-resistant microorganisms. Expert Rev Anti Infect Ther 2013; 9:653-79. [PMID: 21819331 DOI: 10.1586/eri.11.77] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Multidrug-resistant organisms are an established and growing worldwide public health problem and few therapeutic options remain available. The traditional antimicrobials (glycopeptides) for multidrug-resistant Gram-positive infections are declining in efficacy. New drugs that are presently available are linezolid, daptomicin and tigecycline, which have well-defined indications for severe infections, and talavancin, which is under Phase III trial for hospital-acquired pneumonia. Unfortunately the therapies available for multidrug-resistant Gram-negatives, including carbapenem-resistant Pseudomonas aeruginosa, Acinetobacter baumannii and Enterobacteriaceae, are limited to only colistin and tigecycline. Both of these drugs are still not registered for severe infections, such as hospital acquired pneumonia. Consequently, as confirmed by scientific evidence, a multidisciplinary approach is needed. Surveillance, infection control procedures, isolation and antimicrobial stewardship should be implemented to reduce multidrug-resistant organism diffusion.
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Affiliation(s)
- Giovanni Battista Orsi
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Roma, Italy
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van Kleef E, Robotham JV, Jit M, Deeny SR, Edmunds WJ. Modelling the transmission of healthcare associated infections: a systematic review. BMC Infect Dis 2013; 13:294. [PMID: 23809195 PMCID: PMC3701468 DOI: 10.1186/1471-2334-13-294] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 06/21/2013] [Indexed: 11/22/2022] Open
Abstract
Background Dynamic transmission models are increasingly being used to improve our understanding of the epidemiology of healthcare-associated infections (HCAI). However, there has been no recent comprehensive review of this emerging field. This paper summarises how mathematical models have informed the field of HCAI and how methods have developed over time. Methods MEDLINE, EMBASE, Scopus, CINAHL plus and Global Health databases were systematically searched for dynamic mathematical models of HCAI transmission and/or the dynamics of antimicrobial resistance in healthcare settings. Results In total, 96 papers met the eligibility criteria. The main research themes considered were evaluation of infection control effectiveness (64%), variability in transmission routes (7%), the impact of movement patterns between healthcare institutes (5%), the development of antimicrobial resistance (3%), and strain competitiveness or co-colonisation with different strains (3%). Methicillin-resistant Staphylococcus aureus was the most commonly modelled HCAI (34%), followed by vancomycin resistant enterococci (16%). Other common HCAIs, e.g. Clostridum difficile, were rarely investigated (3%). Very few models have been published on HCAI from low or middle-income countries. The first HCAI model has looked at antimicrobial resistance in hospital settings using compartmental deterministic approaches. Stochastic models (which include the role of chance in the transmission process) are becoming increasingly common. Model calibration (inference of unknown parameters by fitting models to data) and sensitivity analysis are comparatively uncommon, occurring in 35% and 36% of studies respectively, but their application is increasing. Only 5% of models compared their predictions to external data. Conclusions Transmission models have been used to understand complex systems and to predict the impact of control policies. Methods have generally improved, with an increased use of stochastic models, and more advanced methods for formal model fitting and sensitivity analyses. Insights gained from these models could be broadened to a wider range of pathogens and settings. Improvements in the availability of data and statistical methods could enhance the predictive ability of models.
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Affiliation(s)
- Esther van Kleef
- Infectious Disease Epidemiology Department, Faculty of Epidemiology and Population Health, Centre of Mathematical Modelling, London School of Hygiene and Tropical Medicine, London, UK.
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Teodoro D, Lovis C. Empirical mode decomposition and k-nearest embedding vectors for timely analyses of antibiotic resistance trends. PLoS One 2013; 8:e61180. [PMID: 23637796 PMCID: PMC3636283 DOI: 10.1371/journal.pone.0061180] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 03/07/2013] [Indexed: 12/03/2022] Open
Abstract
Background Antibiotic resistance is a major worldwide public health concern. In clinical settings, timely antibiotic resistance information is key for care providers as it allows appropriate targeted treatment or improved empirical treatment when the specific results of the patient are not yet available. Objective To improve antibiotic resistance trend analysis algorithms by building a novel, fully data-driven forecasting method from the combination of trend extraction and machine learning models for enhanced biosurveillance systems. Methods We investigate a robust model for extraction and forecasting of antibiotic resistance trends using a decade of microbiology data. Our method consists of breaking down the resistance time series into independent oscillatory components via the empirical mode decomposition technique. The resulting waveforms describing intrinsic resistance trends serve as the input for the forecasting algorithm. The algorithm applies the delay coordinate embedding theorem together with the k-nearest neighbor framework to project mappings from past events into the future dimension and estimate the resistance levels. Results The algorithms that decompose the resistance time series and filter out high frequency components showed statistically significant performance improvements in comparison with a benchmark random walk model. We present further qualitative use-cases of antibiotic resistance trend extraction, where empirical mode decomposition was applied to highlight the specificities of the resistance trends. Conclusion The decomposition of the raw signal was found not only to yield valuable insight into the resistance evolution, but also to produce novel models of resistance forecasters with boosted prediction performance, which could be utilized as a complementary method in the analysis of antibiotic resistance trends.
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Affiliation(s)
- Douglas Teodoro
- Division of Medical Information Sciences, University Hospitals of Geneva, Geneva, Switzerland.
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Choudhury R, Panda S, Singh DV. Emergence and dissemination of antibiotic resistance: a global problem. Indian J Med Microbiol 2013. [PMID: 23183460 DOI: 10.4103/0255-0857.103756] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibiotic resistance is a major problem in clinical health settings. Interestingly the origin of many of antibiotic resistance mechanisms can be traced back to non-pathogenic environmental organisms. Important factors leading to the emergence and spread of antibiotic resistance include absence of regulation in the use of antibiotics, improper waste disposal and associated transmission of antibiotic resistance genes in the community through commensals. In this review, we discussed the impact of globalisation on the transmission of antibiotic resistance genes in bacteria through immigration and export/import of foodstuff. The significance of surveillance to define appropriate use of antibiotics in the clinic has been included as an important preventive measure.
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Affiliation(s)
- R Choudhury
- Infectious Disease Biology, Institute of Life Sciences, Nalco Square, Bhubaneswar-751 023, Odisha, India
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Age and other risk factors of pneumonia among residents of Polish long-term care facilities. Int J Infect Dis 2013; 17:e37-43. [DOI: 10.1016/j.ijid.2012.07.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 05/24/2012] [Accepted: 07/04/2012] [Indexed: 11/20/2022] Open
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Youssef DA, Ranasinghe T, Grant WB, Peiris AN. Vitamin D's potential to reduce the risk of hospital-acquired infections. DERMATO-ENDOCRINOLOGY 2012; 4:167-75. [PMID: 22928073 PMCID: PMC3427196 DOI: 10.4161/derm.20789] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Health care–associated and hospital-acquired infections are two entities associated with increased morbidity and mortality. They are highly costly and constitute a great burden to the health care system. Vitamin D deficiency (< 20 ng/ml) is prevalent and may be a key contributor to both acute and chronic ill health. Vitamin D deficiency is associated with decreased innate immunity and increased risk for infections. Vitamin D can positively influence a wide variety of microbial infections.
Herein we discuss hospital-acquired infections, such as pneumonia, bacteremias, urinary tract and surgical site infections, and the potential role vitamin D may play in ameliorating them. We also discuss how vitamin D might positively influence these infections and help contain health care costs. Pending further studies, we think it is prudent to check vitamin D status at hospital admission and to take immediate steps to address existing insufficient 25-hydroxyvitamin D levels.
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Joyner ML, Manning CC, Canter BN. Modeling the effects of introducing a new antibiotic in a hospital setting: A case study. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2012; 9:601-625. [PMID: 22881028 DOI: 10.3934/mbe.2012.9.601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The increase in antibiotic resistance continues to pose a public health risk as very few new antibiotics are being produced, and bacteria resistant to currently prescribed antibiotics is growing. Within a typical hospital setting, one may find patients colonized with bacteria resistant to a single antibiotic, or, of a more emergent threat, patients may be colonized with bacteria resistant to multiple antibiotics. Precautions have been implemented to try to prevent the growth and spread of antimicrobial resistance such as a reduction in the distribution of antibiotics and increased hand washing and barrier preventions; however, the rise of this resistance is still evident. As a result, there is a new movement to try to re-examine the need for the development of new antibiotics. In this paper, we use mathematical models to study the possible benefits of implementing a new antibiotic in this setting; through these models, we examine the use of a new antibiotic that is distributed in various ways and how this could reduce total resistance in the hospital. We compare several different models in which patients colonized with both single and dual-resistant bacteria are present, including a model with no additional treatment protocols for the population colonized with dual-resistant bacteria as well as models including isolation and/or treatment with a new antibiotic. We examine the benefits and limitations of each scenario in the simulations presented.
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Affiliation(s)
- Michele L Joyner
- Department of Mathematics and Statistics and Institute for Quantitative Biology, East Tennessee State University, Johnson City, TN, United States.
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