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Pople D, Kypraios T, Donker T, Stoesser N, Seale AC, George R, Dodgson A, Freeman R, Hope R, Walker AS, Hopkins S, Robotham J. Model-based evaluation of admission screening strategies for the detection and control of carbapenemase-producing Enterobacterales in the English hospital setting. BMC Med 2023; 21:492. [PMID: 38087343 PMCID: PMC10717398 DOI: 10.1186/s12916-023-03007-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Globally, detections of carbapenemase-producing Enterobacterales (CPE) colonisations and infections are increasing. The spread of these highly resistant bacteria poses a serious threat to public health. However, understanding of CPE transmission and evidence on effectiveness of control measures is severely lacking. This paper provides evidence to inform effective admission screening protocols, which could be important in controlling nosocomial CPE transmission. METHODS CPE transmission within an English hospital setting was simulated with a data-driven individual-based mathematical model. This model was used to evaluate the ability of the 2016 England CPE screening recommendations, and of potential alternative protocols, to identify patients with CPE-colonisation on admission (including those colonised during previous stays or from elsewhere). The model included nosocomial transmission from colonised and infected patients, as well as environmental contamination. Model parameters were estimated using primary data where possible, including estimation of transmission using detailed epidemiological data within a Bayesian framework. Separate models were parameterised to represent hospitals in English areas with low and high CPE risk (based on prevalence). RESULTS The proportion of truly colonised admissions which met the 2016 screening criteria was 43% in low-prevalence and 54% in high-prevalence areas respectively. Selection of CPE carriers for screening was improved in low-prevalence areas by adding readmission as a screening criterion, which doubled how many colonised admissions were selected. A minority of CPE carriers were confirmed as CPE positive during their hospital stay (10 and 14% in low- and high-prevalence areas); switching to a faster screening test pathway with a single-swab test (rather than three swab regimen) increased the overall positive predictive value with negligible reduction in negative predictive value. CONCLUSIONS Using a novel within-hospital CPE transmission model, this study assesses CPE admission screening protocols, across the range of CPE prevalence observed in England. It identifies protocol changes-adding readmissions to screening criteria and a single-swab test pathway-which could detect similar numbers of CPE carriers (or twice as many in low CPE prevalence areas), but faster, and hence with lower demand on pre-emptive infection-control resources. Study findings can inform interventions to control this emerging threat, although further work is required to understand within-hospital transmission sources.
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Affiliation(s)
- Diane Pople
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.
| | - Theodore Kypraios
- School of Mathematical Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Tjibbe Donker
- University Medical Center Freiburg, Institute for Infection Prevention and Hospital Epidemiology, Breisacher Strasse, 79106, Freiburg im Breisgau, Germany
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare Associated Infections, University of Oxford and UKHSA, Oxford, UK
| | - Anna C Seale
- University of Warwick, Warwick, UK
- London School of Hygiene & Tropical Medicine, London, UK
- UK Health Security Agency, London, UK
| | - Ryan George
- Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew Dodgson
- UK Health Security Agency, Manchester Public Health Laboratory, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL, UK
| | - Rachel Freeman
- IQVIA, The Point, 37 North Wharf Road, London, W2 1AF, UK
| | - Russell Hope
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susan Hopkins
- NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare Associated Infections, University of Oxford and UKHSA, Oxford, UK
- UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK
- Division of Infection and Immunity, UCL, Gower St, London, UK
| | - Julie Robotham
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK
- NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare Associated Infections, University of Oxford and UKHSA, Oxford, UK
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2
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Lapp Z, Octaria R, O’Malley SM, Nguyen TN, Wolford H, Crawford R, Moore C, Snippes Vagnone P, Noel D, Duffy N, Pirani A, Thomas LS, Pattee B, Pearson C, Bulens SN, Hoffman S, Kainer M, Anacker M, Meek J, See I, Gontjes KJ, Chan A, Lynfield R, Maloney M, Hayden MK, Snitkin E, Slayton RB. Distinct Origins and Transmission Pathways of blaKPC Enterobacterales across Three U.S. States. J Clin Microbiol 2023; 61:e0025923. [PMID: 37439675 PMCID: PMC10446861 DOI: 10.1128/jcm.00259-23] [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: 03/06/2023] [Accepted: 06/27/2023] [Indexed: 07/14/2023] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) are among the most concerning antibiotic resistance threats due to high rates of multidrug resistance, transmissibility in health care settings, and high mortality rates. We evaluated the potential for regional genomic surveillance to track the spread of blaKPC-carrying CRE (KPC-CRE) by using isolate collections from health care facilities in three U.S. states. Clinical isolates were collected from Connecticut (2017 to 2018), Minnesota (2012 to 2018), and Tennessee (2016 to 2017) through the U.S. Centers for Disease Control and Prevention's Multi-site Gram-negative Surveillance Initiative (MuGSI) and additional surveillance. KPC-CRE isolates were whole-genome sequenced, yielding 255 isolates from 214 patients across 96 facilities. Case report data on patient comorbidities, facility exposures, and interfacility patient transfer were extracted. We observed that in Connecticut, most KPC-CRE isolates showed evidence of importation from outside the state, with limited local transmission. In Minnesota, cases were mainly from sporadic importation and transmission of blaKPC-carrying Klebsiella pneumoniae ST258, and clonal expansion of blaKPC-carrying Enterobacter hormaechei ST171, primarily at a single focal facility and its satellite facilities. In Tennessee, we observed transmission of diverse strains of blaKPC-carrying Enterobacter and Klesbiella, with evidence that most derived from the local acquisition of blaKPC plasmids circulating in an interconnected regional health care network. Thus, the underlying processes driving KPC-CRE burden can differ substantially across regions and can be discerned through regional genomic surveillance. This study provides proof of concept that integrating genomic data with information on interfacility patient transfers can provide insights into locations and drivers of regional KPC-CRE burden that can enable targeted interventions.
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Affiliation(s)
- Zena Lapp
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Rany Octaria
- Department of Medicine, Division of Epidemiology, Vanderbilt University, Nashville, Tennessee, USA
- Tennessee Department of Health, Nashville, Tennessee, USA
| | | | - Tu Ngoc Nguyen
- Connecticut Department of Public Health, Hartford, Connecticut, USA
| | - Hannah Wolford
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ryan Crawford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Diane Noel
- Connecticut Department of Public Health, Hartford, Connecticut, USA
| | - Nadezhda Duffy
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ali Pirani
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Claire Pearson
- Connecticut Department of Public Health, Hartford, Connecticut, USA
| | - Sandra N. Bulens
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sophie Hoffman
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Marion Kainer
- Tennessee Department of Health, Nashville, Tennessee, USA
| | | | - James Meek
- Connecticut Emerging Infections Program, Yale School of Public Health, New Haven, Connecticut, USA
| | - Isaac See
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kyle J. Gontjes
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Allison Chan
- Tennessee Department of Health, Nashville, Tennessee, USA
| | - Ruth Lynfield
- Minnesota Department of Health, Saint Paul, Minnesota, USA
| | - Meghan Maloney
- Connecticut Department of Public Health, Hartford, Connecticut, USA
| | - Mary K. Hayden
- Department of Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois, USA
- Department of Pathology, Rush University Medical Center, Chicago, Illinois, USA
| | - Evan Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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3
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Manoukian S, Stewart S, Dancer SJ, Mason H, Graves N, Robertson C, Leonard A, Kennedy S, Kavanagh K, Parcell B, Reilly J. Probabilistic microsimulation to examine the cost-effectiveness of hospital admission screening strategies for carbapenemase-producing enterobacteriaceae (CPE) in the United Kingdom. THE EUROPEAN JOURNAL OF HEALTH ECONOMICS : HEPAC : HEALTH ECONOMICS IN PREVENTION AND CARE 2022; 23:1173-1185. [PMID: 34932169 PMCID: PMC8689289 DOI: 10.1007/s10198-021-01419-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Antimicrobial resistance has been recognised as a global threat with carbapenemase- producing-Enterobacteriaceae (CPE) as a prime example. CPE has similarities to COVID-19 where asymptomatic patients may be colonised representing a source for onward transmission. There are limited treatment options for CPE infection leading to poor outcomes and increased costs. Admission screening can prevent cross-transmission by pre-emptively isolating colonised patients. OBJECTIVE We assess the relative cost-effectiveness of screening programmes compared with no- screening. METHODS A microsimulation parameterised with NHS Scotland date was used to model scenarios of the prevalence of CPE colonised patients on admission. Screening strategies were (a) two-step screening involving a clinical risk assessment (CRA) checklist followed by microbiological testing of high-risk patients; and (b) universal screening. Strategies were considered with either culture or polymerase chain reaction (PCR) tests. All costs were reported in 2019 UK pounds with a healthcare system perspective. RESULTS In the low prevalence scenario, no screening had the highest probability of cost-effectiveness. Among screening strategies, the two CRA screening options were the most likely to be cost-effective. Screening was more likely to be cost-effective than no screening in the prevalence of 1 CPE colonised in 500 admitted patients or more. There was substantial uncertainty with the probabilities rarely exceeding 40% and similar results between strategies. Screening reduced non-isolated bed-days and CPE colonisation. The cost of screening was low in relation to total costs. CONCLUSION The specificity of the CRA checklist was the parameter with the highest impact on the cost-effectiveness. Further primary data collection is needed to build models with less uncertainty in the parameters.
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Affiliation(s)
- Sarkis Manoukian
- Yunus Centre for Social Business and Health, Glasgow Caledonian University, Glasgow, Scotland, UK.
| | - Sally Stewart
- Safeguarding Health Through Infection Prevention Research Group, Glasgow Caledonian University, Glasgow, Scotland, UK
| | - Stephanie J Dancer
- Department of Microbiology, Hairmyres Hospital, NHS Lanarkshire and School of Applied Sciences, Edinburgh Napier University, Edinburgh, Scotland, UK
| | - Helen Mason
- Yunus Centre for Social Business and Health, Glasgow Caledonian University, Glasgow, Scotland, UK
| | | | - Chris Robertson
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, Scotland, UK
| | | | - Sharon Kennedy
- Information Services Division, Public Health Scotland, Edinburgh, Scotland, UK
| | - Kim Kavanagh
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, Scotland, UK
| | - Benjamin Parcell
- Medical Microbiology, NHS Tayside, Ninewells Hospital and School of Medicine, Dundee, Scotland, UK
| | - Jacqui Reilly
- Safeguarding Health Through Infection Prevention Research Group, Glasgow Caledonian University, Glasgow, Scotland, UK
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4
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Tadese BK, Darkoh C, DeSantis SM, Mgbere O, Fujimoto K. Clinical Epidemiology of Carbapenem-Resistant Enterobacterales in the Greater Houston Region of Texas: A 6-year Trend and Surveillance Analysis. J Glob Antimicrob Resist 2022; 30:222-227. [PMID: 35764216 PMCID: PMC9486688 DOI: 10.1016/j.jgar.2022.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/30/2022] [Accepted: 06/21/2022] [Indexed: 11/25/2022] Open
Abstract
Objectives: Carbapenem-resistant Enterobacterales (CRE) remain an urgent public health priority in the United States. CRE poses a major threat to patients in healthcare and a potential risk to the community. This study examined the epidemiological trends, clinical, and microbiological data of CRE in the Greater Houston region of Texas. Methods: A multi-institutional retrospective observational study was conducted using surveillance data collected from 2015 to 2020. Predictors of incidence rates of CRE were determined by a negative binomial regression fit using a generalized estimation equation. Results: Over a 6-year period, 4236 CRE cases were reported, of which Klebsiella pneumoniae accounted for 84.8%. The results show a steady increase in CRE cases, with a sharp rise since 2018. The majority of carbapenemase-producing Enterobacterales were Klebsiella pneumoniae carbapenemase (KPC)-producing (77.2%), followed by other rare carbapenemases, which includes OXA-48, NDM, IMP, VIM, coproduction of KPC with OXA-48, KPC with NDM, and NDM with OXA-48. Acute care hospitals (ACH) accounted for 68.5% of the source of CRE cases. The incidence rate of CRE cases reported from ACH and long-term acute care (LTAC) facilities was 1.16 times that of long-term care facilities (adjusted rate ratio [ARR] = 1.16, 95% confidence interval [CI]:1.04–1.30). The incidence rate of CRE among patients with indwelling devices was 15% (ARR = 0.85, 95% CI: 0.79–0.92) lower than that of patients without indwelling devices. Conclusion: The rise in the rate of CRE cases despite aggressive infection prevention and control strategies in the region is alarming. Evaluating and improving the current infection control strategies may be warranted.
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Affiliation(s)
- Bekana K Tadese
- University of Texas Health Science Center, School of Public Health, Center for Infectious Diseases, Houston, Texas, USA; Fort Bend County Health and Human Services, Texas, USA
| | - Charles Darkoh
- University of Texas Health Science Center, School of Public Health, Center for Infectious Diseases, Houston, Texas, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Microbiology, and Infectious Diseases Program, Houston, Texas, USA.
| | - Stacia M DeSantis
- University of Texas Health Science Center, School of Public Health, Center for Infectious Diseases, Houston, Texas, USA
| | - Osaro Mgbere
- Disease Prevention and Control Division, Houston Health Department, Houston, Texas, USA; Institute of Community Health, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Kayo Fujimoto
- University of Texas Health Science Center, School of Public Health, Center for Infectious Diseases, Houston, Texas, USA
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5
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Salamzade R, Manson AL, Walker BJ, Brennan-Krohn T, Worby CJ, Ma P, He LL, Shea TP, Qu J, Chapman SB, Howe W, Young SK, Wurster JI, Delaney ML, Kanjilal S, Onderdonk AB, Bittencourt CE, Gussin GM, Kim D, Peterson EM, Ferraro MJ, Hooper DC, Shenoy ES, Cuomo CA, Cosimi LA, Huang SS, Kirby JE, Pierce VM, Bhattacharyya RP, Earl AM. Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance. Genome Med 2022; 14:37. [PMID: 35379360 PMCID: PMC8981930 DOI: 10.1186/s13073-022-01040-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/22/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms. METHODS To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years. RESULTS Our CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment. CONCLUSIONS Collectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.
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Affiliation(s)
- Rauf Salamzade
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.14003.360000 0001 2167 3675Present Address: Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Abigail L. Manson
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Bruce J. Walker
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,Applied Invention, Cambridge, MA 02139 USA
| | - Thea Brennan-Krohn
- grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Colin J. Worby
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Peijun Ma
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Lorrie L. He
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Terrance P. Shea
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - James Qu
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Sinéad B. Chapman
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Whitney Howe
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Sarah K. Young
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Jenna I. Wurster
- grid.38142.3c000000041936754XDepartment of Ophthalmology, Department of Microbiology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, 240 Charles St., Boston, MA 02114 USA
| | - Mary L. Delaney
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Sanjat Kanjilal
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Healthcare Institute, Boston, MA 02215 USA
| | - Andrew B. Onderdonk
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Cassiana E. Bittencourt
- grid.266093.80000 0001 0668 7243Department of Pathology and Laboratory Medicine, University of California Irvine School of Medicine, Orange, CA 92868 USA
| | - Gabrielle M. Gussin
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - Diane Kim
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - Ellena M. Peterson
- grid.266093.80000 0001 0668 7243Department of Pathology and Laboratory Medicine, University of California Irvine School of Medicine, Orange, CA 92868 USA
| | - Mary Jane Ferraro
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - David C. Hooper
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Erica S. Shenoy
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Christina A. Cuomo
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Lisa A. Cosimi
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Susan S. Huang
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - James E. Kirby
- grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Virginia M. Pierce
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Roby P. Bhattacharyya
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Ashlee M. Earl
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
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6
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Mills JP, Marchaim D. Multidrug-Resistant Gram-Negative Bacteria: Infection Prevention and Control Update. Infect Dis Clin North Am 2021; 35:969-994. [PMID: 34752228 DOI: 10.1016/j.idc.2021.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Multidrug-resistant gram-negative bacteria (MDR-GNB) pose one of the greatest challenges to health care today because of their propensity for human-to-human transmission and lack of therapeutic options. Containing the spread of MDR-GNB is challenging, and the application of multifaceted infection control bundles during an evolving outbreak makes it difficult to measure the relative impact of each measure. This article will review the utility of various infection control measures in containing the spread of various MDR-GNB and will provide the supporting evidence for these interventions.
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Affiliation(s)
- John P Mills
- Division of Infectious Diseases, University of Michigan Medical School, F4177 University Hospital South, 1500 E. Medical Center Dr, Ann Arbor, MI 48109-5226, USA.
| | - Dror Marchaim
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Division of Infectious Diseases, Shamir (Assaf Harofeh) Medical Center, Zerifin, Israel
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7
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Dai Y, Meng T, Wang X, Tang B, Wang F, Du Y, Qiu Y, Liu J, Tan R, Qu H. Validation and Extrapolation of a Multimodal Infection Prevention and Control Intervention on Carbapenem-Resistant Klebsiella pneumoniae in an Epidemic Region: A Historical Control Quasi-Experimental Study. Front Med (Lausanne) 2021; 8:692813. [PMID: 34307419 PMCID: PMC8292674 DOI: 10.3389/fmed.2021.692813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/11/2021] [Indexed: 11/25/2022] Open
Abstract
Objective: To verify the effects of comprehensive infection prevention and control (IPC) interventions for the prevention of the cross-transmission of carbapenem-resistant Klebsiella pneumoniae (CRKP) within intensive care units (ICUs) in an epidemic region. Methods: A historical control, quasi-experimental design was performed. The study was conducted between January 2017 and December 2019, following the implementation of a multimodal IPC bundle. The baseline period was established from January 2013 to June 2013, when only basic IPC measures were applied. Results: A total of 748 patients were enrolled during the entire study. The incidence of ICU-acquired CRKP colonization/infection was 1.16 per 1,000 patient-days during the intervention period, compared with 10.19 per 1,000 patient-days during the baseline period (p = 0.002). The slope of the monthly incidence of CRKP at admission showed an increasing trend (p = 0.03). The incidence of ICU-acquired catheter-related bloodstream infections caused by CRKP decreased from 2.54 to 0.96 per 1,000 central-line-days (p = 0.08). Compliance with contact precautions and terminal room disinfection improved during the intervention period. All environmental surface culture samples acquired after terminal room disinfection were negative for CRKP. Conclusion: Our findings suggest that in epidemic settings, multimodal IPC intervention strategies and consistent monitoring of compliance, may limit the spread of CRKP in ICUs.
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Affiliation(s)
- Yunqi Dai
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Tianjiao Meng
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaoli Wang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Bin Tang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Feng Wang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ying Du
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yuzhen Qiu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jialin Liu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ruoming Tan
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hongping Qu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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8
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Lapp Z, Han JH, Wiens J, Goldstein EJC, Lautenbach E, Snitkin ES. Patient and Microbial Genomic Factors Associated with Carbapenem-Resistant Klebsiella pneumoniae Extraintestinal Colonization and Infection. mSystems 2021; 6:e00177-21. [PMID: 33727393 PMCID: PMC8546970 DOI: 10.1128/msystems.00177-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/30/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical-priority antibiotic resistance threat that has emerged over the past several decades, spread across the globe, and accumulated resistance to last-line antibiotic agents. While CRKP infections are associated with high mortality, only a subset of patients acquiring CRKP extraintestinal colonization will develop clinical infection. Here, we sought to ascertain the relative importance of patient characteristics and CRKP genetic background in determining patient risk of infection. Machine learning models classifying colonization versus infection were built using whole-genome sequences and clinical metadata from a comprehensive set of 331 CRKP extraintestinal isolates collected across 21 long-term acute-care hospitals over the course of a year. Model performance was evaluated based on area under the receiver operating characteristic curve (AUROC) on held-out test data. We found that patient and genomic features were predictive of clinical CRKP infection to similar extents (AUROC interquartile ranges [IQRs]: patient = 0.59 to 0.68, genomic = 0.55 to 0.61, combined = 0.62 to 0.68). Patient predictors of infection included the presence of indwelling devices, kidney disease, and length of stay. Genomic predictors of infection included presence of the ICEKp10 mobile genetic element carrying the yersiniabactin iron acquisition system and disruption of an O-antigen biosynthetic gene in a sublineage of the epidemic ST258 clone. Altered O-antigen biosynthesis increased association with the respiratory tract, and subsequent ICEKp10 acquisition was associated with increased virulence. These results highlight the potential of integrated models including both patient and microbial features to provide a more holistic understanding of patient clinical trajectories and ongoing within-lineage pathogen adaptation.IMPORTANCE Multidrug-resistant organisms, such as carbapenem-resistant Klebsiella pneumoniae (CRKP), colonize alarmingly large fractions of patients in regions of endemicity, but only a subset of patients develop life-threatening infections. While patient characteristics influence risk for infection, the relative contribution of microbial genetic background to patient risk remains unclear. We used machine learning to determine whether patient and/or microbial characteristics can discriminate between CRKP extraintestinal colonization and infection across multiple health care facilities and found that both patient and microbial factors were predictive. Examination of informative microbial genetic features revealed variation within the ST258 epidemic lineage that was associated with respiratory tract colonization and increased rates of infection. These findings indicate that circulating genetic variation within a highly prevalent epidemic lineage of CRKP influences patient clinical trajectories. In addition, this work supports the need for future studies examining the microbial genetic determinants of clinical outcomes in human populations, as well as epidemiologic and experimental follow-ups of identified features to discern generalizability and biological mechanisms.
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Affiliation(s)
- Zena Lapp
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Jenna Wiens
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, USA
| | - Ellie J C Goldstein
- R. M. Alden Research Laboratory, Culver City, California, USA
- David Geffen School of Medicine, University of California, Los Angeles, Santa Monica, California, USA
| | - Ebbing Lautenbach
- Department of Medicine (Infectious Diseases), University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
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9
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Lee BY, Bartsch SM, Lin MY, Asti L, Welling J, Mueller LE, Leonard J, Brown ST, Doshi K, Kemble SK, Mitgang EA, Weinstein RA, Trick WE, Hayden MK. How Long-Term Acute Care Hospitals Can Play an Important Role in Controlling Carbapenem-Resistant Enterobacteriaceae in a Region: A Simulation Modeling Study. Am J Epidemiol 2021; 190:448-458. [PMID: 33145594 DOI: 10.1093/aje/kwaa247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 11/14/2022] Open
Abstract
Typically, long-term acute care hospitals (LTACHs) have less experience in and incentives to implementing aggressive infection control for drug-resistant organisms such as carbapenem-resistant Enterobacteriaceae (CRE) than acute care hospitals. Decision makers need to understand how implementing control measures in LTACHs can impact CRE spread regionwide. Using our Chicago metropolitan region agent-based model to simulate CRE spread and control, we estimated that a prevention bundle in only LTACHs decreased prevalence by a relative 4.6%-17.1%, averted 1,090-2,795 new carriers, 273-722 infections and 37-87 deaths over 3 years and saved $30.5-$69.1 million, compared with no CRE control measures. When LTACHs and intensive care units intervened, prevalence decreased by a relative 21.2%. Adding LTACHs averted an additional 1,995 carriers, 513 infections, and 62 deaths, and saved $47.6 million beyond implementation in intensive care units alone. Thus, LTACHs may be more important than other acute care settings for controlling CRE, and regional efforts to control drug-resistant organisms should start with LTACHs as a centerpiece.
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10
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Bartsch SM, Wong KF, Stokes-Cawley OJ, McKinnell JA, Cao C, Gussin GM, Mueller LE, Kim DS, Miller LG, Huang SS, Lee BY. Knowing More of the Iceberg: How Detecting a Greater Proportion of Carbapenem-Resistant Enterobacteriaceae Carriers Influences Transmission. J Infect Dis 2020; 221:1782-1794. [PMID: 31150539 PMCID: PMC7213567 DOI: 10.1093/infdis/jiz288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/30/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Clinical testing detects a fraction of carbapenem-resistant Enterobacteriaceae (CRE) carriers. Detecting a greater proportion could lead to increased use of infection prevention and control measures but requires resources. Therefore, it is important to understand the impact of detecting increasing proportions of CRE carriers. METHODS We used our Regional Healthcare Ecosystem Analyst-generated agent-based model of adult inpatient healthcare facilities in Orange County, California, to explore the impact that detecting greater proportions of carriers has on the spread of CRE. RESULTS Detecting and placing 1 in 9 carriers on contact precautions increased the prevalence of CRE from 0% to 8.0% countywide over 10 years. Increasing the proportion of detected carriers from 1 in 9 up to 1 in 5 yielded linear reductions in transmission; at proportions >1 in 5, reductions were greater than linear. Transmission reductions did not occur for 1, 4, or 5 years, varying by facility type. With a contact precautions effectiveness of ≤70%, the detection level yielding nonlinear reductions remained unchanged; with an effectiveness of >80%, detecting only 1 in 5 carriers garnered large reductions in the number of new CRE carriers. Trends held when CRE was already present in the region. CONCLUSION Although detection of all carriers provided the most benefits for preventing new CRE carriers, if this is not feasible, it may be worthwhile to aim for detecting >1 in 5 carriers.
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Affiliation(s)
- Sarah M Bartsch
- Public Health Computational and Operations Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Global Obesity Prevention Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Kim F Wong
- Center for Simulation and Modeling, University of Pittsburgh, Pennsylvania
| | - Owen J Stokes-Cawley
- Public Health Computational and Operations Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Global Obesity Prevention Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - James A McKinnell
- Infectious Disease Clinical Outcomes Research Unit, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Los Angeles, California
- Torrance Memorial Medical Center, Torrance, California
| | - Chenghua Cao
- Division of Infectious Diseases, University of California–Irvine Health School of Medicine, Irvine, California
- Health Policy Research Institute, University of California–Irvine Health School of Medicine, Irvine, California
| | - Gabrielle M Gussin
- Division of Infectious Diseases, University of California–Irvine Health School of Medicine, Irvine, California
- Health Policy Research Institute, University of California–Irvine Health School of Medicine, Irvine, California
| | - Leslie E Mueller
- Public Health Computational and Operations Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Global Obesity Prevention Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Diane S Kim
- Division of Infectious Diseases, University of California–Irvine Health School of Medicine, Irvine, California
- Health Policy Research Institute, University of California–Irvine Health School of Medicine, Irvine, California
| | | | - Susan S Huang
- Division of Infectious Diseases, University of California–Irvine Health School of Medicine, Irvine, California
- Health Policy Research Institute, University of California–Irvine Health School of Medicine, Irvine, California
| | - Bruce Y Lee
- Public Health Computational and Operations Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Global Obesity Prevention Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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11
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Whole-Genome Sequencing To Identify Drivers of Carbapenem-Resistant Klebsiella pneumoniae Transmission within and between Regional Long-Term Acute-Care Hospitals. Antimicrob Agents Chemother 2019; 63:AAC.01622-19. [PMID: 31451495 DOI: 10.1128/aac.01622-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/16/2019] [Indexed: 12/17/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an antibiotic resistance threat of the highest priority. Given the limited treatment options for this multidrug-resistant organism (MDRO), there is an urgent need for targeted strategies to prevent transmission. Here, we applied whole-genome sequencing to a comprehensive collection of clinical isolates to reconstruct regional transmission pathways and analyzed this transmission network in the context of statewide patient transfer data and patient-level clinical data to identify drivers of regional transmission. We found that high regional CRKP burdens were due to a small number of regional introductions, with subsequent regional proliferation occurring via patient transfers among health care facilities. While CRKP was predicted to have been imported into each facility multiple times, there was substantial variation in the ratio of intrafacility transmission events per importation, indicating that amplification occurs unevenly across regional facilities. While myriad factors likely influence intrafacility transmission rates, an understudied one is the potential for clinical characteristics of colonized and infected patients to influence their propensity for transmission. Supporting the contribution of high-risk patients to elevated transmission rates, we observed that patients colonized and infected with CRKP in high-transmission facilities had higher rates of carbapenem use, malnutrition, and dialysis and were older. This report highlights the potential for regional infection prevention efforts that are grounded in genomic epidemiology to identify the patients and facilities that make the greatest contribution to regional MDRO prevalence, thereby facilitating the design of precision interventions of maximal impact.
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12
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Abstract
The Clinical and Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing agree that carbapenemase testing is not necessary for clinical care, provided that the laboratory is up to date with current breakpoints. Nonetheless, publication on the development and modification of carbapenemase tests continues, as is the case in this issue of the Journal of Clinical Microbiology (R. W. Beresford and M. Maley, J Clin Microbiol 57:e01852-18, 2019, https://doi.org/10.1128/JCM.01852-18). This commentary explores modifications to the carbapenem inactivation method-but is this the right focus for clinical laboratories?
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