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Tracy KC, McKaig J, Kinnear C, Millar J, King AA, Read AF, Woods RJ. Reversion to sensitivity explains limited transmission of resistance in a hospital pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597162. [PMID: 38895443 PMCID: PMC11185621 DOI: 10.1101/2024.06.03.597162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Bacterial pathogens that are successful in hospital environments must survive times of intense antibiotic exposure and times of no antibiotic exposure. When these organisms are closely associated with human hosts, they must also transmit from one patient to another for the resistance to spread. The resulting evolutionary dynamics have, in some settings, led to rising levels of resistance in hospitals. Here, we focus on an important but understudied aspect of this dynamic: the loss of resistance when the resistant organisms evolve in environments where the antibiotic pressure is removed. Based on prior data, we hypothesize that resistance arising in the context of strong selection may carry a high cost and revert to sensitivity quickly once the selective pressure is removed. Conversely, resistant isolates that persist through times of no antibiotic pressure should carry a lower cost and revert less quickly. To test this hypothesis, we utilize a genetically diverse set of patient-derived, daptomycin-resistant Enterococcus faecium isolates that include cases of both de novo emergence of resistance within patients and putatively transmitted resistance. Both of these sets of strains have survived periods of antibiotic exposure, but only putatively transmitted resistant strains have survived extended periods without antibiotic exposure. These strains were then allowed to evolve in antibiotic free laboratory conditions. We find that putatively transmitted resistant strains tended to have lower level resistance but that evolution in antibiotic-free conditions resulted in minimal loss of resistance. In contrast, resistance that arose de novo within patients was higher level but exhibited greater declines in resistance in vitro. Sequencing of the experimentally evolved isolates revealed that reversal of high level resistance resulted from evolutionary pathways that were frequently genetically associated with the unique resistance mutations of that strain. Thus, the rapid reversal of high-level resistance was associated with accessible evolutionary pathways where an increase in fitness is associated with decreased resistance. We describe how this rapid loss of resistance may limit the spread of resistance within the hospital and shape the diversity of resistance phenotypes across patients.
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Affiliation(s)
- Kevin C. Tracy
- Department of Computational Medicine and Bioinformatics, University of Michigan
| | | | - Clare Kinnear
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan
| | - Jess Millar
- Department of Computational Medicine and Bioinformatics, University of Michigan
| | - Aaron A. King
- Department of Ecology and Evolutionary Biology, University of Michigan
- Center for the Study of Complex Systems, University of Michigan
- The Santa Fe Institute
| | - Andrew F. Read
- Department of Biology, Pennsylvania State University
- Department of Entomology, Pennsylvania State University
| | - Robert J. Woods
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan
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Chanderraj R, Baker JM, Kay SG, Brown CA, Hinkle KJ, Fergle DJ, McDonald RA, Falkowski NR, Metcalf JD, Kaye KS, Woods RJ, Prescott HC, Sjoding MW, Dickson RP. Reply to: Anti-anaerobic antibiotics: indication is key. Eur Respir J 2023; 61:61/5/2300492. [PMID: 37169381 DOI: 10.1183/13993003.00492-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 05/13/2023]
Affiliation(s)
- Rishi Chanderraj
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Medicine Service, Infectious Diseases Section, Veterans Affairs (VA) Ann Arbor Healthcare System, Ann Arbor, MI, USA
| | - Jennifer M Baker
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stephen G Kay
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Brown
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Research on Innovation and Science, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kevin J Hinkle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel J Fergle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Roderick A McDonald
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicole R Falkowski
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joseph D Metcalf
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Keith S Kaye
- Division of Infectious Diseases, Department of Medicine, Rutgers-New Jersey Medical School, Newark, NJ, USA
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Medicine Service, Infectious Diseases Section, Veterans Affairs (VA) Ann Arbor Healthcare System, Ann Arbor, MI, USA
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Hallie C Prescott
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI, USA
- VA Center for Clinical Management Research, Ann Arbor, MI, USA
| | - Michael W Sjoding
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Institute for Healthcare Policy and Innovation, University of Michigan, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research & Innovation, Ann Arbor, MI, USA
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- Weil Institute for Critical Care Research & Innovation, Ann Arbor, MI, USA
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Kajova M, Khawaja T, Kantele A. European hospitals as source of multidrug-resistant bacteria: analysis of travellers screened in Finland after hospitalization abroad. J Travel Med 2022; 29:6540946. [PMID: 35234907 PMCID: PMC9282090 DOI: 10.1093/jtm/taac022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/01/2022] [Accepted: 02/06/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND As hospitals have a high prevalence of multidrug-resistant organisms (MDRO), hospitalization abroad indicates for travellers an increased risk of acquiring MDRO-and carrying the strains home. Antimicrobial resistance (AMR) rates are highest in the (sub)tropics, whereas Europe is considered a lower risk region. Since AMR prevalences vary within Europe, we aimed to gather country-specific data on the risks for hospitalized travellers. METHODS At hospitals of the Helsinki and Uusimaa district in Finland, patients hospitalized abroad over the past 12 months are systematically screened for methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE), carbapenemase-producing bacteria and vancomycin-resistant Enterococcus spp. (VRE). Among patients screened 2010-19, we selected those hospitalized in Europe, recorded their MDRO findings, infections and mortality, and analysed MDRO-associated risk factors. RESULTS Of the 1772 patients treated in 41 European countries, 16.6% (295) carried MDRO, 12.5% (221) ESBL-PE, 7.8% (138) solely ESBL-E. coli, 2.6% (46) MRSA, 2.2% (30) of those screened VRE and 2.2% (39) carbapenem-resistant Gram-negatives. Among those colonized, 9.8% (29) had symptomatic MDRO infections and 0.3% (one) died. Colonization was most frequently recorded for those treated in eastern and southern Europe, with Bulgaria, Cyprus and the Russian Federation scoring highest. MDRO colonization was associated with antibiotic treatment and showed a negative correlation with time from discharge to screening. CONCLUSIONS After hospitalization in European countries, ESBL-PE carriage was relatively common (12.5%), while other MDROs proved less frequent (<5%). Antibiotic treatment and short time since hospitalization abroad increased the risk of MDRO colonization. Clear differences between countries and regions were revealed, with highest rates in the east and the south.
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Affiliation(s)
- Mikael Kajova
- Department of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
| | - Tamim Khawaja
- Department of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
| | - Anu Kantele
- Department of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland.,Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Biehl LM, Higgins PG, Stemler J, Gilles M, Peter S, Dörfel D, Vogel W, Kern WV, Gölz H, Bertz H, Rohde H, Klupp EM, Schafhausen P, Salmanton-García J, Stecher M, Wille J, Liss B, Xanthopoulou K, Zweigner J, Seifert H, Vehreschild MJGT. Impact of single-room contact precautions on acquisition and transmission of vancomycin-resistant enterococci on haematological and oncological wards, multicentre cohort-study, Germany, January-December 2016. Euro Surveill 2022; 27:2001876. [PMID: 35027104 PMCID: PMC8759111 DOI: 10.2807/1560-7917.es.2022.27.2.2001876] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 08/18/2021] [Indexed: 06/14/2023] Open
Abstract
BackgroundEvidence supporting the effectiveness of single-room contact precautions (SCP) in preventing in-hospital acquisition of vancomycin-resistant enterococci (haVRE) is limited.AimWe assessed the impact of SCP on haVRE and their transmission.MethodsWe conducted a prospective, multicentre cohort study in German haematological/oncological departments during 2016. Two sites performed SCP for VRE patients and two did not (NCP). We defined a 5% haVRE-risk difference as non-inferiority margin, screened patients for VRE, and characterised isolates by whole genome sequencing and core genome MLST (cgMLST). Potential confounders were assessed by competing risk regression analysis.ResultsWe included 1,397 patients at NCP and 1,531 patients at SCP sites. Not performing SCP was associated with a significantly higher proportion of haVRE; 12.2% (170/1,397) patients at NCP and 7.4% (113/1,531) patients at SCP sites (relative risk (RR) 1.74; 95% confidence interval (CI): 1.35-2.23). The difference (4.8%) was below the non-inferiority margin. Competing risk regression analysis indicated a stronger impact of antimicrobial exposure (subdistribution hazard ratio (SHR) 7.46; 95% CI: 4.59-12.12) and underlying disease (SHR for acute leukaemia 2.34; 95% CI: 1.46-3.75) on haVRE than NCP (SHR 1.60; 95% CI: 1.14-2.25). Based on cgMLST and patient movement data, we observed 131 patient-to-patient VRE transmissions at NCP and 85 at SCP sites (RR 1.76; 95% CI: 1.33-2.34).ConclusionsWe show a positive impact of SCP on haVRE in a high-risk population, although the observed difference was below the pre-specified non-inferiority margin. Importantly, other factors including antimicrobial exposure seem to be more influential.
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Affiliation(s)
- Lena M Biehl
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, partner site Bonn-Cologne, Germany
| | - Paul G Higgins
- German Centre for Infection Research, partner site Bonn-Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Jannik Stemler
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, partner site Bonn-Cologne, Germany
| | - Meyke Gilles
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research, partner site Tübingen, Germany
| | - Daniela Dörfel
- Department of Haematology, Oncology and Immunology, Siloah hospital, Hannover, Germany
| | - Wichard Vogel
- Department of Oncology, Haematology, Immunology and Rheumatology, Internal Medicine II, University Hospital Tübingen, Tübingen, Germany
| | - Winfried V Kern
- Division of Infectious Diseases, Department of Medicine II, University Medical Centre, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hanna Gölz
- Institute for Medical Microbiology and Hygiene, University Medical Centre, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hartmut Bertz
- Department of Haematology, Oncology and Stem Cell Transplantation, University Medical Centre, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Germany
- German Centre for Infection Research, partner site Hamburg-Lübeck-Borstel, Germany
| | - Eva-Maria Klupp
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Germany
| | - Philippe Schafhausen
- Department of Oncology and Haematology, Hubertus Wald Tumorzentrum/University Cancer Centre Hamburg, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Jon Salmanton-García
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Melanie Stecher
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, partner site Bonn-Cologne, Germany
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Blasius Liss
- Department I of Internal Medicine, Helios University Hospital Wuppertal, Wuppertal, Germany
- Department of Internal medicine I, School of Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Janine Zweigner
- Department of Hospital Hygiene and Infection Control, University Hospital of Cologne, Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Harald Seifert
- German Centre for Infection Research, partner site Bonn-Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Maria J G T Vehreschild
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
- German Centre for Infection Research, partner site Bonn-Cologne, Germany
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Kajova M, Khawaja T, Kangas J, Mäkinen H, Kantele A. Import of multidrug-resistant bacteria from abroad through interhospital transfers, Finland, 2010-2019. ACTA ACUST UNITED AC 2021; 26. [PMID: 34596014 PMCID: PMC8485579 DOI: 10.2807/1560-7917.es.2021.26.39.2001360] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background While 20–80% of regular visitors to (sub)tropical regions become colonised by extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE), those hospitalised abroad often also carry other multidrug-resistant (MDR) bacteria on return; the rates are presumed to be highest for interhospital transfers. Aim This observational study assessed MDR bacterial colonisation among patients transferred directly from hospitals abroad to Helsinki University Hospital. We investigated predisposing factors, clinical infections and associated fatalities. Methods Data were derived from screening and from diagnostic samples collected between 2010 and 2019. Risk factors of colonisation were identified by multivariable analysis. Microbiologically verified symptomatic infections and infection-related mortality were recorded during post-transfer hospitalisation. Results Colonisation rates proved highest for transfers from Asia (69/96; 71.9%) and lowest for those within Europe (99/524; 18.9%). Of all 698 patients, 208 (29.8%) were colonised; among those, 163 (78.4%) carried ESBL-PE, 28 (13.5%) MDR Acinetobacter species, 25 (12.0%) meticillin-resistant Staphylococcus aureus, 25 (12.0%) vancomycin-resistant Enterococcus, 14 (6.7%) carbapenemase-producing Enterobacteriaceae, and 12 (5.8%) MDR Pseudomonas aeruginosa; 46 strains tested carbapenemase gene-positive. In multivariable analysis, geographical region, intensive care unit (ICU) treatment and antibiotic use abroad proved to be risk factors for colonisation. Clinical MDR infections, two of them fatal (1.0%), were recorded for 22 of 208 (10.6%) MDR carriers. Conclusions Colonisation by MDR bacteria was common among patients transferred from foreign hospitals. Region of hospitalisation, ICU treatment and antibiotic use were identified as predisposing factors. Within 30 days after transfer, MDR colonisation manifested as clinical infection in more than 10% of the carriers.
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Affiliation(s)
- Mikael Kajova
- Inflammation Center, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tamim Khawaja
- Inflammation Center, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jonas Kangas
- Inflammation Center, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hilda Mäkinen
- Inflammation Center, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anu Kantele
- Inflammation Center, Department of Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Transmission dynamics of a linear vanA-plasmid during a nosocomial multiclonal outbreak of vancomycin-resistant enterococci in a non-endemic area, Japan. Sci Rep 2021; 11:14780. [PMID: 34285270 PMCID: PMC8292306 DOI: 10.1038/s41598-021-94213-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
The spread of vancomycin-resistant enterococci (VRE) is a major threat in nosocomial settings. A large-scale multiclonal VRE outbreak has rarely been reported in Japan due to low VRE prevalence. We evaluated the transmission of vancomycin resistance in a multiclonal VRE outbreak, conducted biological and genomic analyses of VRE isolates, and assessed the implemented infection control measures. In total, 149 patients harboring VanA-type VRE were identified from April 2017 to October 2019, with 153 vancomycin-resistant Enterococcus faecium isolated being grouped into 31 pulsotypes using pulsed-field gel electrophoresis, wherein six sequence types belonged to clonal complex 17. Epidemic clones varied throughout the outbreak; however, they all carried vanA-plasmids (pIHVA). pIHVA is a linear plasmid, carrying a unique structural Tn1546 containing vanA; it moves between different Enterococcus spp. by genetic rearrangements. VRE infection incidence among patients in the "hot spot" ward correlated with the local VRE colonization prevalence. Local prevalence also correlated with vancomycin usage in the ward. Transmission of a novel transferrable vanA-plasmid among Enterococcus spp. resulted in genomic diversity in VRE in a non-endemic setting. The prevalence of VRE colonization and vancomycin usage at the ward level may serve as VRE cross-transmission indicators in non-intensive care units for outbreak control.
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Kinnear CL, Hansen E, Morley VJ, Tracy KC, Forstchen M, Read AF, Woods RJ. Daptomycin treatment impacts resistance in off-target populations of vancomycin-resistant Enterococcus faecium. PLoS Biol 2020; 18:e3000987. [PMID: 33332354 PMCID: PMC7775125 DOI: 10.1371/journal.pbio.3000987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 12/31/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022] Open
Abstract
The antimicrobial resistance crisis has persisted despite broad attempts at intervention. It has been proposed that an important driver of resistance is selection imposed on bacterial populations that are not the intended target of antimicrobial therapy. But to date, there has been limited quantitative measure of the mean and variance of resistance following antibiotic exposure. Here we focus on the important nosocomial pathogen Enterococcus faecium in a hospital system where resistance to daptomycin is evolving despite standard interventions. We hypothesized that the intravenous use of daptomycin generates off-target selection for resistance in transmissible gastrointestinal (carriage) populations of E. faecium. We performed a cohort study in which the daptomycin resistance of E. faecium isolated from rectal swabs from daptomycin-exposed patients was compared to a control group of patients exposed to linezolid, a drug with similar indications. In the daptomycin-exposed group, daptomycin resistance of E. faecium from the off-target population was on average 50% higher than resistance in the control group (n = 428 clones from 22 patients). There was also greater phenotypic diversity in daptomycin resistance within daptomycin-exposed patients. In patients where multiple samples over time were available, a wide variability in temporal dynamics were observed, from long-term maintenance of resistance to rapid return to sensitivity after daptomycin treatment stopped. Sequencing of isolates from a subset of patients supports the argument that selection occurs within patients. Our results demonstrate that off-target gastrointestinal populations rapidly respond to intravenous antibiotic exposure. Focusing on the off-target evolutionary dynamics may offer novel avenues to slow the spread of antibiotic resistance.
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Affiliation(s)
- Clare L. Kinnear
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Elsa Hansen
- Center for Infectious Disease Dynamics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Valerie J. Morley
- Center for Infectious Disease Dynamics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kevin C. Tracy
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Meghan Forstchen
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrew F. Read
- Center for Infectious Disease Dynamics and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Huck Institutes of the Life Sciences and Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Robert J. Woods
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, United States of America
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8
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Abstract
The Centers for Disease Control and Prevention estimates that VRE causes an estimated 54,000 infections and 539 million dollars in attributable health care costs annually. Despite improvements in hand washing, environmental cleaning, and antibiotic use, VRE is still prevalent in many hospitals. There is a pressing need to better understand the processes by which patients acquire VRE. Multiple lines of evidence suggest that intestinal microbiota may help some patients resist VRE acquisition. In this large case-control study, we compared the 16S profile of intestinal microbiota on admission in patients that did and did not subsequently acquire VRE. The 16S profile did not predict subsequent VRE acquisition, in part due to rapid and dramatic change in the gut microbiome following hospitalization. However, Blautia spp. present on admission predicted decreased Enterococcus abundance after VRE acquisition, and Lactobacillus spp. present on admission predicted Enterococcus dominance after VRE acquisition. Thus, VRE acquisition and domination may be distinct processes. Vancomycin-resistant Enterococcus (VRE) is a leading cause of hospital-acquired infections and continues to spread despite widespread implementation of pathogen-targeted control guidelines. Commensal gut microbiota provide colonization resistance to VRE, but the role of gut microbiota in VRE acquisition in at-risk patients is unknown. To address this gap in our understanding, we performed a case-control study of gut microbiota in hospitalized patients who did (cases) and did not (controls) acquire VRE. We matched case subjects to control subjects by known risk factors and “time at risk,” defined as the time elapsed between admission until positive VRE screen. We characterized gut bacterial communities using 16S rRNA gene amplicon sequencing of rectal swab specimens. We analyzed 236 samples from 59 matched case-control pairs. At baseline, case and control subjects did not differ in gut microbiota when measured by community diversity (P = 0.33) or composition (P = 0.30). After hospitalization, gut communities of cases and controls differed only in the abundance of the Enterococcus-containing operational taxonomic unit (OTU), with the gut microbiota of case subjects having more of this OTU than time-matched control subjects (P = 0.01). Otherwise, case and control communities after the time at risk did not differ in diversity (P = 0.33) or community structure (P = 0.12). Among patients who became VRE colonized, those having the Blautia-containing OTU on admission had lower Enterococcus relative abundance once colonized (P = 0.004). Our results demonstrate that the 16S profile of the gut microbiome does not predict VRE acquisition in hospitalized patients, likely due to rapid and profound microbiota change. The gut microbiome does not predict VRE acquisition, but it may be associated with Enterococcus expansion, suggesting that these should be considered two distinct processes. IMPORTANCE The Centers for Disease Control and Prevention estimates that VRE causes an estimated 54,000 infections and 539 million dollars in attributable health care costs annually. Despite improvements in hand washing, environmental cleaning, and antibiotic use, VRE is still prevalent in many hospitals. There is a pressing need to better understand the processes by which patients acquire VRE. Multiple lines of evidence suggest that intestinal microbiota may help some patients resist VRE acquisition. In this large case-control study, we compared the 16S profile of intestinal microbiota on admission in patients that did and did not subsequently acquire VRE. The 16S profile did not predict subsequent VRE acquisition, in part due to rapid and dramatic change in the gut microbiome following hospitalization. However, Blautia spp. present on admission predicted decreased Enterococcus abundance after VRE acquisition, and Lactobacillus spp. present on admission predicted Enterococcus dominance after VRE acquisition. Thus, VRE acquisition and domination may be distinct processes.
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Zhou S, Barbosa C, Woods RJ. Why is preventing antibiotic resistance so hard? Analysis of failed resistance management. EVOLUTION MEDICINE AND PUBLIC HEALTH 2020; 2020:102-108. [PMID: 32983536 PMCID: PMC7502268 DOI: 10.1093/emph/eoaa020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 12/25/2022]
Abstract
We describe the case of a patient with pancreatitis followed by intra-abdominal infection in which source control was not achieved. Antimicrobial therapy led to the emergence of resistance in multiple organisms through multiple population dynamics processes. While the initial insult was not due to infection, subsequent infections with resistant organisms contributed to a poor outcome for the patient. Though resistance evolution was a known risk, it was difficult to predict the next organism that would arise in the setting of antibiotic pressure and its resistance profile. This case illustrates the clinical challenge of antibiotic resistance that current approaches cannot readily prevent. LAY SUMMARY Why is antibiotic resistance management so complex? Distinct evolutionary processes unfold when antibiotic treatment is initiated that lead, separately and together, to the undesired outcome of antibiotic resistance. This clinical case exemplifies some of those processes and highlights the dire need for evolutionary risk assessments to be incorporated into clinical decision making.
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Affiliation(s)
- Shiwei Zhou
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109-5680, USA
| | - Camilo Barbosa
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109-5680, USA
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109-5680, USA
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So M. Vancomycin-Resistant Enterococcus in Hematology-Oncology Patients: a Review on Colonization, Screening, Infections, Resistance, and Antimicrobial Stewardship. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2020. [DOI: 10.1007/s40506-020-00227-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Willems RPJ, van Dijk K, Ket JCF, Vandenbroucke-Grauls CMJE. Evaluation of the Association Between Gastric Acid Suppression and Risk of Intestinal Colonization With Multidrug-Resistant Microorganisms: A Systematic Review and Meta-analysis. JAMA Intern Med 2020; 180:561-571. [PMID: 32091544 PMCID: PMC7042870 DOI: 10.1001/jamainternmed.2020.0009] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
IMPORTANCE Acid suppressants inhibit gastric acid secretion and disrupt the intestinal microbiome. Whether acid suppression increases the risk of colonization with multidrug-resistant microorganisms (MDROs) is unclear. OBJECTIVES To systematically examine the association of use of acid suppressants with the risk of colonization with MDROs and to perform a meta-analysis of current evidence. DATA SOURCES PubMed, Embase, the Web of Science Core Collection, and the Cochrane Central Register of Controlled Trials were searched from database inception through July 8, 2019. STUDY SELECTION Study selection was performed independently by 2 authors (R.P.J.W. and C.M.J.E.V.-G.) on the basis of predefined selection criteria; conflicts were resolved by consensus or by an adjudicator (K.v.D.). Human observational studies (case control, cohort, and cross-sectional) and clinical trial designs were selected if they quantified the risk of MDRO colonization in users of acid suppressants in comparison with nonusers. DATA EXTRACTION AND SYNTHESIS The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) and Meta-analysis of Observational Studies in Epidemiology (MOOSE) recommendations were followed. Data were extracted independently by the same 2 authors, and adjudication was conducted when necessary. Risk of bias was assessed according to a modified Newcastle-Ottawa Scale. Pooled odds ratios (ORs) were estimated using random-effects models; heterogeneity was evaluated using the I2 method. MAIN OUTCOMES AND MEASURES The primary outcome measure was intestinal colonization with MDROs of the Enterobacterales order (producing extended-spectrum β-lactamases, carbapenemases, or plasmid-mediated AmpC β-lactamases), vancomycin-resistant enterococci, methicillin-resistant or vancomycin-resistant Staphylococcus aureus, or multidrug-resistant Pseudomonas or Acinetobacter species. RESULTS A total of 26 observational studies including 29 382 patients (11 439 [38.9%] acid suppressant users) met the selection criteria. Primary meta-analysis of 12 studies including 22 305 patients that provided adjusted ORs showed that acid suppression increased the odds of intestinal carriage of MDROs of the Enterobacterales order and of vancomycin-resistant enterococci by roughly 75% (OR = 1.74; 95% CI, 1.40-2.16; I2 = 68%). The odds were concordant with the secondary pooled analysis of all 26 studies (OR = 1.70; 95% CI, 1.44-1.99; I2 = 54%). Heterogeneity was partially explained by variations in study setting and the type of acid suppression. CONCLUSIONS AND RELEVANCE Acid suppression is associated with increased odds of MDRO colonization. Notwithstanding the limitations of observational studies, the association is plausible and is strengthened by controlling for confounders. In view of the global increase in antimicrobial resistance, stewardship to reduce unnecessary use of acid suppressants may help to prevent MDRO colonization.
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Affiliation(s)
- Roel P J Willems
- Amsterdam Infection and Immunity Institute, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Karin van Dijk
- Amsterdam Infection and Immunity Institute, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Johannes C F Ket
- Medical Library, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Christina M J E Vandenbroucke-Grauls
- Amsterdam Infection and Immunity Institute, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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Klein EY, Tseng KK, Hinson J, Goodman KE, Smith A, Toerper M, Amoah J, Tamma PD, Levin SR, Milstone AM. The Role of Healthcare Worker-Mediated Contact Networks in the Transmission of Vancomycin-Resistant Enterococci. Open Forum Infect Dis 2020; 7:ofaa056. [PMID: 32166095 PMCID: PMC7060899 DOI: 10.1093/ofid/ofaa056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 02/13/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND User- and time-stamped data from hospital electronic health records (EHRs) present opportunities to evaluate how healthcare worker (HCW)-mediated contact networks impact transmission of multidrug-resistant pathogens, such as vancomycin-resistant enterococci (VRE). METHODS This is a retrospective analysis of incident acquisitions of VRE between July 1, 2016 and June 30, 2018. Clinical and demographic patient data were extracted from the hospital EHR system, including all recorded HCW contacts with patients. Contacts by an HCW with 2 different patients within 1 hour was considered a "connection". Incident VRE acquisition was determined by positive clinical or surveillance cultures collected ≥72 hours after a negative surveillance culture. RESULTS There were 2952 hospitalizations by 2364 patients who had ≥2 VRE surveillance swabs, 112 (4.7%) patients of which had incident nosocomial acquisitions. Patients had a median of 24 (interquartile range [IQR], 18-33) recorded HCW contacts per day, 9 (IQR, 5-16) of which, or approximately 40%, were connections that occurred <1 hour after another patient contact. Patients that acquired VRE had a higher average number of daily connections to VRE-positive patients (3.1 [standard deviation {SD}, 2.4] versus 2.0 [SD, 2.1]). Controlling for other risk factors, connection to a VRE-positive patient was associated with increased odds of acquiring VRE (odds ratio, 1.64; 95% confidence interval, 1.39-1.92). CONCLUSIONS We demonstrated that EHR data can be used to quantify the impact of HCW-mediated patient connections on transmission of VRE in the hospital. Defining incident acquisition risk of multidrug-resistant organisms through HCWs connections from EHR data in real-time may aid implementation and evaluation of interventions to contain their spread.
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Affiliation(s)
- Eili Y Klein
- The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Center for Disease Dynamics, Economics & Policy, Washington, District of Columbia, USA
| | - Katie K Tseng
- Center for Disease Dynamics, Economics & Policy, Washington, District of Columbia, USA
| | - Jeremiah Hinson
- The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Katherine E Goodman
- The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Aria Smith
- The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Matt Toerper
- The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Joe Amoah
- The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Pranita D Tamma
- The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Scott R Levin
- The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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Morley VJ, Woods RJ, Read AF. Bystander Selection for Antimicrobial Resistance: Implications for Patient Health. Trends Microbiol 2019; 27:864-877. [PMID: 31288975 PMCID: PMC7079199 DOI: 10.1016/j.tim.2019.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/29/2019] [Accepted: 06/13/2019] [Indexed: 12/15/2022]
Abstract
Antimicrobial therapy promotes resistance emergence in target infections and in off-target microbiota. Off-target resistance emergence threatens patient health when off-target populations are a source of future infections, as they are for many important drug-resistant pathogens. However, the health risks of antimicrobial exposure in off-target populations remain largely unquantified, making rational antibiotic stewardship challenging. Here, we discuss the contribution of bystander antimicrobial exposure to the resistance crisis, the implications for antimicrobial stewardship, and some novel opportunities to limit resistance evolution while treating target pathogens.
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Affiliation(s)
- Valerie J Morley
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, The Pennsylvania State University, University Park, PA, USA.
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Andrew F Read
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, The Pennsylvania State University, University Park, PA, USA; Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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