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Leclerc QJ, Lindsay JA, Knight GM. Mathematical modelling to study the horizontal transfer of antimicrobial resistance genes in bacteria: current state of the field and recommendations. J R Soc Interface 2019; 16:20190260. [PMID: 31409239 DOI: 10.1098/rsif.2019.0260] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the greatest public health challenges we are currently facing. To develop effective interventions against this, it is essential to understand the processes behind the spread of AMR. These are partly dependent on the dynamics of horizontal transfer of resistance genes between bacteria, which can occur by conjugation (direct contact), transformation (uptake from the environment) or transduction (mediated by bacteriophages). Mathematical modelling is a powerful tool to investigate the dynamics of AMR; however, the extent of its use to study the horizontal transfer of AMR genes is currently unclear. In this systematic review, we searched for mathematical modelling studies that focused on horizontal transfer of AMR genes. We compared their aims and methods using a list of predetermined criteria and used our results to assess the current state of this research field. Of the 43 studies we identified, most focused on the transfer of single genes by conjugation in Escherichia coli in culture and its impact on the bacterial evolutionary dynamics. Our findings highlight the existence of an important research gap in the dynamics of transformation and transduction and the overall public health implications of horizontal transfer of AMR genes. To further develop this field and improve our ability to control AMR, it is essential that we clarify the structural complexity required to study the dynamics of horizontal gene transfer, which will require cooperation between microbiologists and modellers.
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Affiliation(s)
- Quentin J Leclerc
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jodi A Lindsay
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Gwenan M Knight
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
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Quantifying the transmission dynamics of MRSA in the community and healthcare settings in a low-prevalence country. Proc Natl Acad Sci U S A 2019; 116:14599-14605. [PMID: 31262808 PMCID: PMC6642346 DOI: 10.1073/pnas.1900959116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA), traditionally associated with hospitals, is increasingly circulating in the community. This imposes, in turn, a potential burden on hospital infection control due to a more frequent hospitalization of colonized patients. We developed an individual-based model, reproducing community and healthcare settings, to understand the epidemiological drivers of MRSA and the connections between the society and the healthcare institutions. We show that in Norway, a low-prevalence country, the rise of infections is driven by an increasing inflow of cases from abroad rather than by an ongoing epidemic. We demonstrate the major role played by households in transmitting MRSA and show that the burden on hospitals from the growing community circulation is still limited thanks to aggressive infection-control protocols. Methicillin-resistant Staphylococcus aureus (MRSA) is a primarily nosocomial pathogen that, in recent years, has increasingly spread to the general population. The rising prevalence of MRSA in the community implies more frequent introductions in healthcare settings that could jeopardize the effectiveness of infection-control procedures. To investigate the epidemiological dynamics of MRSA in a low-prevalence country, we developed an individual-based model (IBM) reproducing the population’s sociodemography, explicitly representing households, hospitals, and nursing homes. The model was calibrated to surveillance data from the Norwegian national registry (2008–2015) and to published household prevalence data. We estimated an effective reproductive number of 0.68 (95% CI 0.47–0.90), suggesting that the observed rise in MRSA infections is not due to an ongoing epidemic but driven by more frequent acquisitions abroad. As a result of MRSA importations, an almost twofold increase in the prevalence of carriage was estimated over the study period, in 2015 reaching a value of 0.37% (0.25–0.54%) in the community and 1.11% (0.79–1.59%) in hospitalized patients. Household transmission accounted for half of new MRSA acquisitions, indicating this setting as a potential target for preventive strategies. However, nosocomial acquisition was still the primary source of symptomatic disease, which reinforces the importance of hospital-based transmission control. Although our results indicate little reason for concern about MRSA transmission in low-prevalence settings in the immediate future, the increases in importation and global circulation highlight the need for coordinated initiatives to reduce the spread of antibiotic resistance worldwide.
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Eyre DW, Didelot X, Buckley AM, Freeman J, Moura IB, Crook DW, Peto TEA, Walker AS, Wilcox MH, Dingle KE. Clostridium difficile trehalose metabolism variants are common and not associated with adverse patient outcomes when variably present in the same lineage. EBioMedicine 2019; 43:347-355. [PMID: 31036529 PMCID: PMC6558026 DOI: 10.1016/j.ebiom.2019.04.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Clostridium difficile ribotype-027, ribotype-078, and ribotype-017 are virulent and epidemic lineages. Trehalose metabolism variants in these ribotypes, combined with increased human trehalose consumption, have been hypothesised to have contributed to their emergence and virulence. METHODS 5232 previously whole-genome sequenced C. difficile isolates were analysed. Clinical isolates were used to investigate the impact of trehalose metabolism variants on mortality. Import data were used to estimate changes in dietary trehalose. Ribotype-027 virulence was investigated in a clinically reflective gut model. FINDINGS Trehalose metabolism variants found in ribotype-027 and ribotype-017 were widely distributed throughout C. difficile clade-2 and clade-4 in 24/29 (83%) and 10/11 (91%) of sequence types (STs), respectively. The four-gene trehalose metabolism cluster described in ribotype-078 was common in genomes from all five clinically-important C. difficile clades (40/167 [24%] STs). The four-gene cluster was variably present in 208 ribotype-015 infections (98 [47%]); 27/208 (13%) of these patients died within 30-days of diagnosis. Adjusting for age, sex, and infecting ST, there was no association between 30-day all-cause mortality and the four-gene cluster (OR 0.36 [95%CI 0.09-1.34, p = 0.13]). Synthetic trehalose imports in the USA, UK, Germany and the EU were < 1 g/capita/year during 2000-2006, and < 9 g/capita/year 2007-2012, compared with dietary trehalose from natural sources of ~100 g/capita/year. Trehalose supplementation did not increase ribotype-027 virulence in a clinically-validated gut model. INTERPRETATION Trehalose metabolism variants are common in C. difficile. Increases in total dietary trehalose during the early-mid 2000s C. difficile epidemic were likely relatively minimal. Alternative explanations are required to explain why ribotype-027, ribotype-078 and ribotype-017 have been successful. FUNDING National Institute for Health Research. Gut model experiments only: Hayashibara Co. Ltd.
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Affiliation(s)
- David W Eyre
- Big Data Institute, University of Oxford, UK; Nuffield Department of Medicine, University of Oxford, UK.
| | - Xavier Didelot
- School of Life Sciences, Department of Statistics, University of Warwick, UK
| | - Anthony M Buckley
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Jane Freeman
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Ines B Moura
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, UK; National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, UK; National Institutes of Health Research Biomedical Research Centre, University of Oxford, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, UK
| | - Kate E Dingle
- Nuffield Department of Medicine, University of Oxford, UK
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Jones M, Jernigan JA, Evans ME, Roselle GA, Hatfield KM, Samore MH. Vital Signs: Trends in Staphylococcus aureus Infections in Veterans Affairs Medical Centers - United States, 2005-2017. MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT 2019; 68:220-224. [PMID: 30845116 PMCID: PMC6421970 DOI: 10.15585/mmwr.mm6809e2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Introduction By 2007, all Department of Veterans Affairs medical centers (VAMCs) had initiated a multifaceted methicillin-resistant Staphylococcus aureus (MRSA) prevention program. MRSA and methicillin-susceptible S. aureus (MSSA) infection rates among VAMC inpatients from 2005 to 2017 were assessed. Methods Clinical microbiology data from any patient admitted to an acute-care VAMC in the United States from 2005 through 2017 and trends in hospital-acquired MRSA colonization were examined. Results S. aureus infections decreased by 43% overall during the study period (p<0.001), driven primarily by decreases in MRSA, which decreased by 55% (p<0.001), whereas MSSA decreased by 12% (p = 0.003). Hospital-onset MRSA and MSSA infections decreased by 66% (p<0.001) and 19% (p = 0.02), respectively. Community-onset MRSA infections decreased by 41% (p<0.001), whereas MSSA infections showed no significant decline. Acquisition of MRSA colonization decreased 78% during 2008–2017 (17% annually, p<0.001). MRSA infection rates declined more sharply among patients who had negative admission surveillance MRSA screening tests (annual 9.7% decline) compared with those among patients with positive admission MRSA screening tests (4.2%) (p<0.05). Conclusions and Implications for Public Health Practice Significant reductions in S. aureus infection following the VAMC intervention were led primarily by decreases in MRSA. Moreover, MRSA infection declines were much larger among patients not carrying MRSA at the time of admission than among those who were. Taken together, these results suggest that decreased MRSA transmission played a substantial role in reducing overall S. aureus infections at VAMCs. Recent calls to withdraw infection control interventions designed to prevent MRSA transmission might be premature and inadvisable, at least until more is known about effective control of bacterial pathogen transmission in health care settings. Effective S. aureus prevention strategies require a multifaceted approach that includes adherence to current CDC recommendations for preventing not only device- and procedure-associated infections, but also transmission of health care–prevalent strains.
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Vilches TN, Bonesso MF, Guerra HM, Fortaleza CMCB, Park AW, Ferreira CP. The role of intra and inter-hospital patient transfer in the dissemination of heathcare-associated multidrug-resistant pathogens. Epidemics 2018; 26:104-115. [PMID: 30583920 DOI: 10.1016/j.epidem.2018.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 11/28/2022] Open
Abstract
Healthcare-associated infections cause significant patient morbidity and mortality, and contribute to growing healthcare costs, whose effects may be felt most strongly in developing countries. Active surveillance systems, hospital staff compliance, including hand hygiene, and a rational use of antimicrobials are among the important measures to mitigate the spread of healthcare-associated infection within and between hospitals. Klebsiella pneumoniae is an important human pathogen that can spread in hospital settings, with some forms exhibiting drug resistance, including resistance to the carbapenem class of antibiotics, the drugs of last resort for such infections. Focusing on the role of patient movement within and between hospitals on the transmission and incidence of enterobacteria producing the K. pneumoniae Carbapenemase (KPC, an enzyme that inactivates several antimicrobials), we developed a metapopulation model where the connections among hospitals are made using a theoretical hospital network based on Brazilian hospital sizes and locations. The pathogen reproductive number, R0 that measures the average number of new infections caused by a single infectious individual, was calculated in different scenarios defined by both the links between hospital environments (regular wards and intensive care units) and between different hospitals (patient transfer). Numerical simulation was used to illustrate the infection dynamics in this set of scenarios. The sensitivity of R0 to model input parameters, such as hospital connectivity and patient-hospital staff contact rates was also established, highlighting the differential importance of factors amenable to change on pathogen transmission and control.
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Affiliation(s)
- T N Vilches
- São Paulo State University (UNESP), Institute of Biosciences, Department of Biostatistics, 18618-689 Botucatu, Brazil
| | - M F Bonesso
- Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - H M Guerra
- Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - C M C B Fortaleza
- Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - A W Park
- Odum School of Ecology & Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - C P Ferreira
- São Paulo State University (UNESP), Institute of Biosciences, Department of Biostatistics, 18618-689 Botucatu, Brazil.
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Knight GM, Costelloe C, Deeny SR, Moore LSP, Hopkins S, Johnson AP, Robotham JV, Holmes AH. Quantifying where human acquisition of antibiotic resistance occurs: a mathematical modelling study. BMC Med 2018; 16:137. [PMID: 30134939 PMCID: PMC6106940 DOI: 10.1186/s12916-018-1121-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 07/09/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Antibiotic-resistant bacteria (ARB) are selected by the use of antibiotics. The rational design of interventions to reduce levels of antibiotic resistance requires a greater understanding of how and where ARB are acquired. Our aim was to determine whether acquisition of ARB occurs more often in the community or hospital setting. METHODS We used a mathematical model of the natural history of ARB to estimate how many ARB were acquired in each of these two environments, as well as to determine key parameters for further investigation. To do this, we explored a range of realistic parameter combinations and considered a case study of parameters for an important subset of resistant strains in England. RESULTS If we consider all people with ARB in the total population (community and hospital), the majority, under most clinically derived parameter combinations, acquired their resistance in the community, despite higher levels of antibiotic use and transmission of ARB in the hospital. However, if we focus on just the hospital population, under most parameter combinations a greater proportion of this population acquired ARB in the hospital. CONCLUSIONS It is likely that the majority of ARB are being acquired in the community, suggesting that efforts to reduce overall ARB carriage should focus on reducing antibiotic usage and transmission in the community setting. However, our framework highlights the need for better pathogen-specific data on antibiotic exposure, ARB clearance and transmission parameters, as well as the link between carriage of ARB and health impact. This is important to determine whether interventions should target total ARB carriage or hospital-acquired ARB carriage, as the latter often dominated in hospital populations.
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Affiliation(s)
- Gwenan M Knight
- National Institute of Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Diseases, Imperial College London, London, W12 0NN, UK.
| | - Céire Costelloe
- National Institute of Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Diseases, Imperial College London, London, W12 0NN, UK
| | | | - Luke S P Moore
- National Institute of Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Diseases, Imperial College London, London, W12 0NN, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Susan Hopkins
- National Institute of Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Diseases, Imperial College London, London, W12 0NN, UK.,Antimicrobial Resistance Programme, Public Health England, London, UK.,Royal Free London NHS Foundation Trust Healthcare, London, UK.,Division of Healthcare-Associated Infection & Antimicrobial Resistance, National Infection Service, Public Health England, London, UK
| | - Alan P Johnson
- National Institute of Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Diseases, Imperial College London, London, W12 0NN, UK.,Division of Healthcare-Associated Infection & Antimicrobial Resistance, National Infection Service, Public Health England, London, UK
| | - Julie V Robotham
- National Institute of Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Diseases, Imperial College London, London, W12 0NN, UK.,Antimicrobial Resistance Programme, Public Health England, London, UK.,Modelling and Economics Unit, National Infection Service, Public Health England and Health Protection Research Unit in Modelling Methodology, London, UK
| | - Alison H Holmes
- National Institute of Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Diseases, Imperial College London, London, W12 0NN, UK.,Imperial College Healthcare NHS Trust, London, UK
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Clostridium difficile in England: can we stop washing our hands? THE LANCET. INFECTIOUS DISEASES 2017; 17:478. [DOI: 10.1016/s1473-3099(17)30186-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 02/28/2017] [Indexed: 11/22/2022]
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