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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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Axell-House DB, Simar SR, Panesso D, Rincon S, Miller WR, Khan A, Pemberton OA, Valdez L, Nguyen AH, Hood KS, Rydell K, DeTranaltes AM, Jones MN, Atterstrom R, Reyes J, Sahasrabhojane PV, Suleyman G, Zervos M, Shelburne SA, Singh KV, Shamoo Y, Hanson BM, Tran TT, Arias CA. LiaX is a surrogate marker for cell envelope stress and daptomycin non-susceptibility in Enterococcus faecium. Antimicrob Agents Chemother 2024; 68:e0106923. [PMID: 38289081 PMCID: PMC10916372 DOI: 10.1128/aac.01069-23] [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: 08/18/2023] [Accepted: 12/20/2023] [Indexed: 02/12/2024] Open
Abstract
Daptomycin (DAP) is often used as a first-line therapy to treat vancomycin-resistant Enterococcus faecium infections, but emergence of DAP non-susceptibility threatens the effectiveness of this antibiotic. Moreover, current methods to determine DAP minimum inhibitory concentrations (MICs) have poor reproducibility and accuracy. In enterococci, DAP resistance is mediated by the LiaFSR cell membrane stress response system, and deletion of liaR encoding the response regulator results in hypersusceptibility to DAP and antimicrobial peptides. The main genes regulated by LiaR are a cluster of three genes, designated liaXYZ. In Enterococcus faecalis, LiaX is surface-exposed with a C-terminus that functions as a negative regulator of cell membrane remodeling and an N-terminal domain that is released to the extracellular medium where it binds DAP. Thus, in E. faecalis, LiaX functions as a sentinel molecule recognizing DAP and controlling the cell membrane response, but less is known about LiaX in E. faecium. Here, we found that liaX is essential in E. faecium with an activated LiaFSR system. Unlike E. faecalis, E. faecium LiaX is not detected in the extracellular milieu and does not appear to alter phospholipid architecture. We further postulated that LiaX could be used as a surrogate marker for cell envelope activation and non-susceptibility to DAP. For this purpose, we developed and optimized a LiaX enzyme-linked immunosorbent assay (ELISA). We then assessed 86 clinical E. faecium bloodstream isolates for DAP MICs and used whole genome sequencing to assess for substitutions in LiaX. All DAP-resistant clinical strains of E. faecium exhibited elevated LiaX levels. Strikingly, 73% of DAP-susceptible isolates by standard MIC determination also had elevated LiaX ELISAs compared to a well-characterized DAP-susceptible strain. Phylogenetic analyses of predicted amino acid substitutions showed 12 different variants of LiaX without a specific association with DAP MIC or LiaX ELISA values. Our findings also suggest that many E. faecium isolates that test DAP susceptible by standard MIC determination are likely to have an activated cell stress response that may predispose to DAP failure. As LiaX appears to be essential for the cell envelope response to DAP, its detection could prove useful to improve the accuracy of susceptibility testing by anticipating therapeutic failure.
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Affiliation(s)
- Dierdre B. Axell-House
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Shelby R. Simar
- Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, Texas, USA
| | - Diana Panesso
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Sandra Rincon
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - William R. Miller
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Ayesha Khan
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Lizbet Valdez
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - April H. Nguyen
- McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Kara S. Hood
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Kirsten Rydell
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Andrea M. DeTranaltes
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Mary N. Jones
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Rachel Atterstrom
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Pranoti V. Sahasrabhojane
- Department of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Geehan Suleyman
- Department of Internal Medicine, Division of Infectious Diseases, Henry Ford Hospital, Detroit, Michigan, USA
| | - Marcus Zervos
- Department of Internal Medicine, Division of Infectious Diseases, Henry Ford Hospital, Detroit, Michigan, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases, Infection Control, and Employee Health, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kavindra V. Singh
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Yousif Shamoo
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Blake M. Hanson
- Center for Infectious Diseases, University of Texas Health Science Center, School of Public Health, Houston, Texas, USA
| | - Truc T. Tran
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Cesar A. Arias
- Division of Infectious Diseases, Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
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3
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Axell-House DB, Simar SR, Panesso D, Rincon S, Miller WR, Khan A, Pemberton OA, Valdez L, Nguyen AH, Hood KS, Rydell K, DeTranaltes AM, Jones MN, Atterstrom R, Reyes J, Sahasrabhojane PV, Suleyman G, Zervos M, Shelburne SA, Singh KV, Shamoo Y, Hanson BM, Tran TT, Arias CA. LiaX is a surrogate marker for cell-envelope stress and daptomycin non-susceptibility in Enterococcus faecium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.18.553907. [PMID: 37645818 PMCID: PMC10462152 DOI: 10.1101/2023.08.18.553907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Daptomycin (DAP) is often used as a first line therapy to treat vancomycin-resistant Enterococcus faecium (VR Efm ) infections but emergence of DAP non-susceptibility threatens the effectiveness of this antibiotic. Moreover, current methods to determine DAP MICs have poor reproducibility and accuracy. In enterococci, DAP resistance is mediated by the LiaFSR cell membrane stress response system and deletion of liaR encoding the response regulator results in hypersusceptibility to DAP and antimicrobial peptides. The main genes regulated by LiaR are a cluster of three genes, designated liaXYZ . In Enterococcus faecalis , LiaX is surface exposed with a C-terminus that functions as a negative regulator of cell membrane remodeling and an N-terminal domain that is released to the extracellular medium where it binds DAP. Thus, in E. faecalis , LiaX functions as a sentinel molecule recognizing DAP and controlling the cell membrane response, but less is known about LiaX in E. faecium . Here, we found that liaX is essential in E. faecium ( Efm ) with an activated LiaFSR system. Unlike E. faecalis , Efm LiaX is not detected in the extracellular milieu and does not appear to alter phospholipid architecture. We further postulated that LiaX could be used as a surrogate marker for cell envelope activation and non-susceptibility to DAP. For this purpose, we developed and optimized a LiaX ELISA. We then assessed 86 clinical E. faecium BSI isolates for DAP MICs and used whole genome sequencing to assess for substitutions in LiaX. All DAP-R clinical strains of E. faecium exhibited elevated LiaX levels. Strikingly, 73% of DAP-S isolates by standard MIC determination had elevated LiaX ELISAs above the established cut-off. Phylogenetic analyses of predicted amino acid substitutions showed 12 different variants of LiaX without a specific association with DAP MIC or LiaX ELISA values. Our findings also suggest that many Efm isolates that test DAP susceptible by standard MIC determination are likely to have an activated cell stress response that may predispose to DAP failure. As LiaX appears to be essential for the cell envelope response to DAP, its detection could prove useful to improve the accuracy of susceptibility testing by anticipating therapeutic failure.
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Lee RA, Goldman J, Haidar G, Lewis J, Arif S, Hand J, La Hoz RM, Pouch S, Holaday E, Clauss H, Kaye KS, Nellore A. Daptomycin-Resistant Enterococcus Bacteremia Is Associated with Prior Daptomycin Use and Increased Mortality after Liver Transplantation. Open Forum Infect Dis 2022; 9:ofab659. [PMID: 35146044 PMCID: PMC8826376 DOI: 10.1093/ofid/ofab659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background Risk factors for acquisition of vancomycin-resistant Enterococcus (VRE) include immunosuppression, antibiotic exposure, indwelling catheters, and manipulation of the gastrointestinal tract, all of which occur in liver transplant recipients. VRE infections are documented in liver transplantation (LT); however, only one single center study has assessed the impact of daptomycin-resistant Enterococcus (DRE) in this patient population. Methods We conducted a retrospective multicenter cohort study comparing liver transplant recipients with either VRE or DRE bacteremia. The primary outcome was death within 1 year of transplantation. Multivariable logistic regression analyses were performed to calculate adjusted odds ratios for outcomes of interest. Results We identified 139 cases of Enterococcus bacteremia following LT, of which 78% were VRE and 22% were DRE. When adjusted for total intensive care unit days in the first transplant year, liver-kidney transplantation, and calcineurin inhibitor use, patients with DRE bacteremia were 2.65 times more likely to die within 1 year of transplantation (adjusted odds ratio [aOR], 2.648; 95% CI, 1.025–6.840; P = .044). Prior daptomycin exposure was found to be an independent predictor of DRE bacteremia (aOR, 30.62; 95% CI, 10.087–92.955; P < .001). Conclusions In this multicenter study of LT recipients with Enterococcus bacteremia, DRE bacteremia was associated with higher 1-year mortality rates when compared with VRE bacteremia. Our data provide strong support for dedicated infection prevention and antimicrobial stewardship efforts for transplant patients. Further research is needed to support the development of better antibiotics for DRE and practical guidance focusing on identification and prevention of colonization and subsequent infection in liver transplant recipients at high risk for DRE bacteremia.
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Affiliation(s)
- Rachael A Lee
- University of Alabama at Birmingham, Birmingham AL, USA
| | | | - Ghady Haidar
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jessica Lewis
- Medical University of South Carolina, Charleston, SC, USA
| | | | | | - Ricardo M La Hoz
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | | | | | - Anoma Nellore
- University of Alabama at Birmingham, Birmingham AL, USA
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5
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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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Morley VJ, Kinnear CL, Sim DG, Olson SN, Jackson LM, Hansen E, Usher GA, Showalter SA, Pai MP, Woods RJ, Read AF. An adjunctive therapy administered with an antibiotic prevents enrichment of antibiotic-resistant clones of a colonizing opportunistic pathogen. eLife 2020; 9:e58147. [PMID: 33258450 PMCID: PMC7707840 DOI: 10.7554/elife.58147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/29/2020] [Indexed: 12/22/2022] Open
Abstract
A key challenge in antibiotic stewardship is figuring out how to use antibiotics therapeutically without promoting the evolution of antibiotic resistance. Here, we demonstrate proof of concept for an adjunctive therapy that allows intravenous antibiotic treatment without driving the evolution and onward transmission of resistance. We repurposed the FDA-approved bile acid sequestrant cholestyramine, which we show binds the antibiotic daptomycin, as an 'anti-antibiotic' to disable systemically-administered daptomycin reaching the gut. We hypothesized that adjunctive cholestyramine could enable therapeutic daptomycin treatment in the bloodstream, while preventing transmissible resistance emergence in opportunistic pathogens colonizing the gastrointestinal tract. We tested this idea in a mouse model of Enterococcus faecium gastrointestinal tract colonization. In mice treated with daptomycin, adjunctive cholestyramine therapy reduced the fecal shedding of daptomycin-resistant E. faecium by up to 80-fold. These results provide proof of concept for an approach that could reduce the spread of antibiotic resistance for important hospital pathogens.
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Affiliation(s)
- Valerie J Morley
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Clare L Kinnear
- Division of Infectious Diseases, Department of Internal Medicine, University of MichiganAnn ArborUnited States
| | - Derek G Sim
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Samantha N Olson
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Lindsey M Jackson
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Elsa Hansen
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Grace A Usher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Scott A Showalter
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity ParkUnited States
- Department of Chemistry, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Manjunath P Pai
- Department of Clinical Pharmacy, College of Pharmacy, University of MichiganAnn ArborUnited States
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of MichiganAnn ArborUnited States
| | - Andrew F Read
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State UniversityUniversity ParkUnited States
- Huck Institutes for the Life Sciences, The Pennsylvania State UniversityUniversity ParkUnited States
- Department of Entomology, The Pennsylvania State UniversityUniversity ParkUnited States
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