1
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Mansoor AER, O'Neil CA, Kwon JH. The role of microbiome-based therapeutics for the reduction and prevention of antimicrobial-resistant organism colonization. Anaerobe 2023; 83:102772. [PMID: 37572864 DOI: 10.1016/j.anaerobe.2023.102772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
Abstract
The gut is host to a diverse array of microbiota that constitute a complex ecological system crucial to human physiology. Disruptors to the normal host microbiota, such as antimicrobials, can cause a loss of species diversity in the gut, reducing its ability to resist colonization by invading pathogens and potentially leading to colonization with antimicrobial resistant organisms (AROs). ARO negatively impact gut health by disrupting the usual heterogeneity of gut microbiota and have the potential to cause systemic disease. In recent years, fecal microbiota transplantation (FMT) has been increasingly explored in the management of specific disease states such as Clostridioides difficile infection (CDI). Promising data from management of CDI has led to considerable interest in understanding the role of therapeutics to restore the gut microbiota to a healthy state. This review aims to discuss key studies that highlight the current landscape, and explore existing clinical evidence, for the use of FMT and microbiome-based therapeutics in combating intestinal colonization with ARO. We also explore potential future directions of such therapeutics and discuss unaddressed needs in this field that merit further investigation.
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Affiliation(s)
- Armaghan-E-Rehman Mansoor
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, 4523 Clayton Avenue, St. Louis, MO, 63110, USA.
| | - Caroline A O'Neil
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, 4523 Clayton Avenue, St. Louis, MO, 63110, USA.
| | - Jennie H Kwon
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, 4523 Clayton Avenue, St. Louis, MO, 63110, USA.
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2
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Harrigan JJ, Abdallah H, Clarke EL, Oganisian A, Roy JA, Lautenbach E, Reesey E, Wernovsky M, Tolomeo P, Morawski Z, Jacob J, Grippi MA, Kelly BJ. Respiratory microbiome disruption and risk for ventilator-associated lower respiratory tract infection. Clin Infect Dis 2021; 74:1564-1571. [PMID: 34363467 DOI: 10.1093/cid/ciab678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Ventilator-associated lower respiratory tract infection (VA-LRTI) is a common among critically ill patients and has been associated with increased morbidity and mortality. In acute critical illness, respiratory microbiome disruption indices (MDIs) have been shown to predict risk for VA-LRTI, but their utility beyond the first days of critical illness is unknown. We sought to characterize how MDIs previously shown to predict VA-LRTI at initiation of mechanical ventilation change with prolonged mechanical ventilation, and if they remain associated with VA-LRTI risk. METHODS We developed a cohort of 83 subjects admitted to a long-term acute care hospital due to their prolonged dependence on mechanical ventilation; performed dense, longitudinal sampling of the lower respiratory tract, collecting 1066 specimens; and characterized the lower respiratory microbiome by 16S rRNA sequencing as well as total bacterial abundance by 16S rRNA qPCR. RESULTS Cross-sectional MDIs, including low Shannon diversity and high total bacterial abundance, were associated with risk for VA-LRTI, but the associations had wide posterior credible intervals. Persistent lower respiratory microbiome disruption showed a more robust association with VA-LRTI risk, with each day of (base e) Shannon diversity < 2.0 associated with a VA-LRTI odds ratio of 1.36 (95% credible interval 1.10 to 1.72). The observed association was consistent across multiple clinical definitions of VA-LRTI. CONCLUSIONS Cross-sectional MDIs have limited ability to discriminate VA-LRTI risk during prolonged mechanical ventilation, but persistent lower respiratory tract microbiome disruption, best characterized by consecutive days with low Shannon diversity, may identify a population at high risk for infection and may help target infection prevention interventions.
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Affiliation(s)
- James J Harrigan
- Division of Infectious Diseases, Department of Medicine; , Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hatem Abdallah
- Division of Infectious Diseases, Department of Medicine; , Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erik L Clarke
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arman Oganisian
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason A Roy
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Ruthers University, Piscataway, NJ, USA
| | - Ebbing Lautenbach
- Division of Infectious Diseases, Department of Medicine; , Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily Reesey
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Magda Wernovsky
- Division of Infectious Diseases, Department of Medicine; , Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Pam Tolomeo
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zygmunt Morawski
- Good Shepherd Penn-Partners Specialty Hospital, Philadelphia, PA, USA
| | - Jerry Jacob
- Division of Infectious Diseases, Department of Medicine; , Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Good Shepherd Penn-Partners Specialty Hospital, Philadelphia, PA, USA
| | - Michael A Grippi
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Good Shepherd Penn-Partners Specialty Hospital, Philadelphia, PA, USA
| | - Brendan J Kelly
- Division of Infectious Diseases, Department of Medicine; , Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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3
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Ducarmon QR, Kuijper EJ, Olle B. Opportunities and Challenges in Development of Live Biotherapeutic Products to Fight Infections. J Infect Dis 2021; 223:S283-S289. [PMID: 33576793 DOI: 10.1093/infdis/jiaa779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Treatment of bacterial infections with broad-spectrum antibiotics is a strategy severely limited by the decreased ability of the perturbed resident microbiota to control expansion of antibiotic-resistant pathogens. Live biotherapeutic products (LBPs) could provide an alternative to antibiotics in infection control by restoring gut colonization resistance and controlling expansion of resistant strains, an important therapeutic need not being addressed with existing anti-infective drug modalities. We review opportunities and challenges in developing LBPs for multidrug-resistant organisms colonization and infection control, with a focus on commercial fecal microbiota transplantation-like products and defined bacterial consortia, and spanning considerations related to availability of models for rational drug candidate selection and dose regimen selection, good manufacturing practice, intellectual property, and commercial viability.
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Affiliation(s)
- Quinten R Ducarmon
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, the Netherlands.,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Bernat Olle
- Vedanta Biosciences Inc., Cambridge, Massachusetts, USA
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4
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Mamo Y, Woodworth MH, Wang T, Dhere T, Kraft CS. Durability and Long-term Clinical Outcomes of Fecal Microbiota Transplant Treatment in Patients With Recurrent Clostridium difficile Infection. Clin Infect Dis 2019; 66:1705-1711. [PMID: 29272401 DOI: 10.1093/cid/cix1097] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/18/2017] [Indexed: 12/21/2022] Open
Abstract
Background Fecal microbiota transplant (FMT) appears safe and effective for treatment of recurrent Clostridium difficile infection (RCDI). However, durability, long-term clinical outcomes, and patient satisfaction after FMT are not well described. Methods Eligible patients who received FMT for RCDI at Emory Hospital between 1 July 2012 and 31 December 2016 were contacted via telephone for a follow-up survey. Of 190 eligible patients, 137 (72%) completed the survey. Results Median time from last FMT to follow-up was 22 months. Overall, 82% (113/137) of patients at follow-up had no recurrence of C. difficile infection (CDI) post-FMT (non-RCDI group) and 18% (24/137) of patients had CDI post-FMT (RCDI group). Antibiotic exposure for non-CDI infections after FMT was more common in the RCDI group compared to the non-RCDI group (75% vs 38%, P = .0009). Overall, 11% of patients reported improvement or resolution of diagnoses not related to CDI post-FMT, and 33% reported development of a new medical condition or symptom post-FMT. Ninety-five percent of patients (122/128) indicated that they would undergo FMT again, and 70% of these 122 reported that they would prefer FMT to antibiotics as initial treatment if they were to have a CDI recurrence. Conclusions In this follow-up survey of outcomes after FMT at a median of 22 months follow-up, 82% of patients had durable cure of CDI. Patients with recurrence had more post-FMT antibiotic exposure, underscoring the need for thoughtful antibiotic use and a potential role for prophylactic microbiome enrichment to reduce recurrence.
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Affiliation(s)
- Yafet Mamo
- Emory University School of Medicine, Atlanta, Georgia
| | | | - Tiffany Wang
- Emory University School of Medicine, Atlanta, Georgia
| | - Tanvi Dhere
- Division of Digestive Diseases, Emory University, Atlanta, Georgia
| | - Colleen S Kraft
- Division of Infectious Diseases, Emory University, Atlanta, Georgia.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
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5
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Woodworth MH, Hayden MK, Young VB, Kwon JH. The Role of Fecal Microbiota Transplantation in Reducing Intestinal Colonization With Antibiotic-Resistant Organisms: The Current Landscape and Future Directions. Open Forum Infect Dis 2019; 6:ofz288. [PMID: 31363779 PMCID: PMC6667716 DOI: 10.1093/ofid/ofz288] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/14/2019] [Indexed: 12/17/2022] Open
Abstract
The intestinal tract is a recognized reservoir of antibiotic-resistant organisms (ARO), and a potential target for strategies to reduce ARO colonization. Microbiome therapies such as fecal microbiota transplantation (FMT) have been established as an effective treatment for recurrent Clostridioides difficile infection and may be an effective approach for reducing intestinal ARO colonization. In this article, we review the current published literature on the role of FMT for eradication of intestinal ARO colonization, review the potential benefit and limitations of the use of FMT in this setting, and outline a research agenda for the future study of FMT for intestinal ARO colonization.
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Affiliation(s)
- Michael H Woodworth
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, Illinois
| | - Vincent B Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor
| | - Jennie H Kwon
- Division of Infectious Diseases, John T. Milliken Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
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6
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Smibert O, Satlin MJ, Nellore A, Peleg AY. Carbapenem-Resistant Enterobacteriaceae in Solid Organ Transplantation: Management Principles. Curr Infect Dis Rep 2019; 21:26. [PMID: 31183574 DOI: 10.1007/s11908-019-0679-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Carbapenem-resistant Enterobacteriaceae (CRE) have emerged as a worldwide problem. Given their degree of immunosuppression and the level of contact with the healthcare system, solid organ transplant (SOT) recipients are at a disproportionately higher risk of acquisition, colonization, and infection with CRE, and outcomes from infection tend to be worse compared to non-transplant patients. Therapeutic options are limited for CRE infections although several newer agents have recently been approved for use. How well these agents perform in the setting of immunosuppression and SOT is unclear. We sought to review the epidemiology of CRE in SOT and the management principles. RECENT FINDINGS CRE infections are becoming an increasing problem in SOT, and donor-derived infections present a challenge in the peri-transplant period. Newer treatments for CRE are emerging that are less toxic and potentially more effective than prior CRE-active agents, but supportive clinical data are limited. Newer beta-lactamase inhibitors have good activity against KPC carbapenemases, but they lack activity against metallo-beta-lactamases (e.g., NDM). Promising data is emerging with newer agents that have activity against most carbapenemases, but, again, clinical data is needed. Combination therapy in addition to optimal pharmacokinetic and pharmacodynamics may go some way to improve outcomes against these difficult-to-treat organisms. Other novel therapies that prevent the emergence of resistance (oral beta-lactamase inhibitors) and eradication of resistant Gram-negative colonization (fecal microbiota transplant) may eventually become part of a bundle approach to reduce CRE infections in the future. As in non-transplant patients, CRE infections in the transplant setting are challenging to treat and prevent. Infection prevention and control remains crucial to prevent widespread dissemination, and unique challenges exist with donor-derived CRE and how best to manage recipients in the peri-transplant period. Newer treatments are now in early-phase clinical studies, and in vitro activity data are supportive for several agents providing hope for improved outcomes with these typically difficult-to-treat and highly morbid infections in transplant recipients.
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Affiliation(s)
- Olivia Smibert
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia.,Transplant Infectious Disease and Compromised Host Program, Massachusetts General Hospital, Boston, MA, USA
| | - Michael J Satlin
- Division of Infectious Diseases, Weill Cornell Medicine, 1300 York Avenue, New York, NY, USA
| | - Anoma Nellore
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anton Y Peleg
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia. .,Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia.
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Microbiome as a tool and a target in the effort to address antimicrobial resistance. Proc Natl Acad Sci U S A 2019; 115:12902-12910. [PMID: 30559176 DOI: 10.1073/pnas.1717163115] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Reciprocal, intimate relationships between the human microbiome and the host immune system are shaped by past microbial encounters and prepare the host for future ones. Antibiotics and other antimicrobials leave their mark on both the microbiome and host immunity. Antimicrobials alter the structure of the microbiota, expand the host-specific pool of antimicrobial-resistance genes and organisms, degrade the protective effects of the microbiota against invasion by pathogens, and may impair vaccine efficacy. Through these effects on the microbiome they may affect immune responses. Vaccines that exert protective or therapeutic effects against pathogens may reduce the use of antimicrobials, the development and spread of antimicrobial resistance, and the harmful impacts of these drugs on the microbiome. Other strategies involving manipulation of the microbiome to deplete antibiotic-resistant organisms or to enhance immune responses to vaccines may prove valuable in addressing antimicrobial resistance as well. This article describes the intersections of immunity, microbiome and antimicrobial exposure, and the use of vaccines and other alternative strategies for the control and management of antimicrobial resistance.
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8
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Research Agenda for Microbiome Based Research for Multidrug-resistant Organism Prevention in the Veterans Health Administration System. Infect Control Hosp Epidemiol 2018; 39:202-209. [PMID: 29417924 DOI: 10.1017/ice.2017.311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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9
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Effectiveness of Probiotic for Primary Prevention of Clostridium difficile Infection: A Single-Center Before-and-After Quality Improvement Intervention at a Tertiary-Care Medical Center. Infect Control Hosp Epidemiol 2018; 39:765-770. [PMID: 29695310 DOI: 10.1017/ice.2018.76] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVETo evaluate probiotics for the primary prevention of Clostridium difficile infection (CDI) among hospital inpatients.DESIGNA before-and-after quality improvement intervention comparing 12-month baseline and intervention periods.SETTINGA 694-bed teaching hospital.INTERVENTIONWe administered a multispecies probiotic comprising L. acidophilus (CL1285), L. casei (LBC80R), and L. rhamnosus (CLR2) to eligible antibiotic recipients within 12 hours of initial antibiotic receipt through 5 days after final dose. We excluded (1) all patients on neonatal, pediatric and oncology wards; (2) all individuals receiving perioperative prophylactic antibiotic recipients; (3) all those restricted from oral intake; and (4) those with pancreatitis, leukopenia, or posttransplant. We defined CDI by symptoms plus C. difficile toxin detection by polymerase chain reaction. Our primary outcome was hospital-onset CDI incidence on eligible hospital units, analyzed using segmented regression.RESULTSThe study included 251 CDI episodes among 360,016 patient days during the baseline and intervention periods, and the incidence rate was 7.0 per 10,000 patient days. The incidence rate was similar during baseline and intervention periods (6.9 vs 7.0 per 10,000 patient days; P=.95). However, compared to the first 6 months of the intervention, we detected a significant decrease in CDI during the final 6 months (incidence rate ratio, 0.6; 95% confidence interval, 0.4-0.9; P=.009). Testing intensity remained stable between the baseline and intervention periods: 19% versus 20% of stools tested were C. difficile positive by PCR, respectively. From medical record reviews, only 26% of eligible patients received a probiotic per the protocol.CONCLUSIONSDespite poor adherence to the protocol, there was a reduction in the incidence of CDI during the intervention, which was delayed ~6 months after introducing probiotic for primary prevention.Infect Control Hosp Epidemiol 2018;765-770.
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10
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Wang T, Kraft CS, Woodworth MH, Dhere T, Eaton ME. Fecal Microbiota Transplant for Refractory Clostridium difficile Infection Interrupts 25-Year History of Recurrent Urinary Tract Infections. Open Forum Infect Dis 2018; 5:ofy016. [PMID: 29450212 PMCID: PMC5808805 DOI: 10.1093/ofid/ofy016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/12/2018] [Indexed: 01/23/2023] Open
Affiliation(s)
- Tiffany Wang
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - Colleen S Kraft
- Emory University School of Medicine, Atlanta, Georgia.,Division of Digestive Diseases, Department of Medicine
| | | | | | - Molly E Eaton
- Emory University School of Medicine, Atlanta, Georgia
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11
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Araos R, Montgomery V, Ugalde JA, Snyder GM, D’Agata EMC. Microbial Disruption Indices to Detect Colonization With Multidrug-Resistant Organisms. Infect Control Hosp Epidemiol 2017; 38:1312-1318. [PMID: 28899445 PMCID: PMC6262892 DOI: 10.1017/ice.2017.190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To characterize the microbial disruption indices of hospitalized patients to predict colonization with multidrug-resistant organisms (MDROs). DESIGN A cross-sectional survey of the fecal microbiome was conducted in a tertiary referral, acute-care hospital in Boston, Massachusetts. PARTICIPANTS The study population consisted of adult patients hospitalized in general medical/surgical wards. METHODS Rectal swabs were obtained from patients within 48 hours of hospital admission and screened for MDRO colonization using conventional culture techniques. The V4 region of the 16S rRNA gene was sequenced to assess the fecal microbiome. Microbial diversity and composition, as well as the functional potential of the microbial communities present in fecal samples, were compared between patients with and without MDRO colonization. RESULTS A total of 44 patients were included in the study, of whom 11 (25%) were colonized with at least 1 MDRO. Reduced microbial diversity and high abundance of metabolic pathways associated with multidrug-resistance mechanisms characterized the fecal microbiome of patients colonized with MDRO at hospital admission. CONCLUSIONS Our data suggest that microbial disruption indices may be key to predicting MDRO colonization and could provide novel infection control approaches. Infect Control Hosp Epidemiol 2017;38:1312-1318.
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Affiliation(s)
- Rafael Araos
- Genomics and Resistant Microbes (GeRM) Group, Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Veronica Montgomery
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Juan A. Ugalde
- Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Graham M. Snyder
- Department of Medicine, Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA
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12
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Galloway-Peña JR, Jenq RR, Shelburne SA. Can Consideration of the Microbiome Improve Antimicrobial Utilization and Treatment Outcomes in the Oncology Patient? Clin Cancer Res 2017; 23:3263-3268. [PMID: 28298544 PMCID: PMC5496798 DOI: 10.1158/1078-0432.ccr-16-3173] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/25/2017] [Accepted: 03/10/2017] [Indexed: 12/24/2022]
Abstract
The need to provide effective and timely antimicrobial treatment to cancer patients with infections is well recognized but tempered by preliminary, but accumulating, evidence that antibiotic-induced microbiome dysbiosis affects cancer therapy response, noninfectious toxicities, and infectious complications. Given only a minority of empirically treated cancer patients are proven to have a true bacterial infection, it is important to consider the potential negative consequences of extensive broad-spectrum antimicrobial use on the commensal microbiota. Herein, we review the literature substantiating the dilemma oncologists face when treating suspected or documented infections with respect to the interaction between the host microbiome, antibiotics, and cancer-related clinical outcomes. We propose microbiome-based explorations that could assist oncologists in optimizing treatment strategies for cancer-related infections as well as the cancer itself. In addition, we discuss knowledge gaps and challenges in this nascent field that must be addressed to deliver medically relevant, translational applications. We anticipate that the emerging knowledge regarding the role of the microbiota in the health of cancer patients may cause a reappraisal of the manner in which antibiotics are used in the oncologic setting and how microorganisms are viewed by oncologists. Clin Cancer Res; 23(13); 3263-8. ©2017 AACRSee related commentary by Fessler and Gajewski, p. 3229.
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Affiliation(s)
- Jessica R Galloway-Peña
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Robert R Jenq
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Samuel A Shelburne
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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13
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Huss J. Fecal Transplant Bioethics: Beyond Chicken Little. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2017; 17:48-50. [PMID: 28430058 DOI: 10.1080/15265161.2017.1299254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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14
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Galloway-Peña JR, Smith DP, Sahasrabhojane P, Wadsworth WD, Fellman BM, Ajami NJ, Shpall EJ, Daver N, Guindani M, Petrosino JF, Kontoyiannis DP, Shelburne SA. Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients. Genome Med 2017; 9:21. [PMID: 28245856 PMCID: PMC5331640 DOI: 10.1186/s13073-017-0409-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/11/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Understanding longitudinal variability of the microbiome in ill patients is critical to moving microbiome-based measurements and therapeutics into clinical practice. However, the vast majority of data regarding microbiome stability are derived from healthy subjects. Herein, we sought to determine intra-patient temporal microbiota variability, the factors driving such variability, and its clinical impact in an extensive longitudinal cohort of hospitalized cancer patients during chemotherapy. METHODS The stool (n = 365) and oral (n = 483) samples of 59 patients with acute myeloid leukemia (AML) undergoing induction chemotherapy (IC) were sampled from initiation of chemotherapy until neutrophil recovery. Microbiome characterization was performed via analysis of 16S rRNA gene sequencing. Temporal variability was determined using coefficients of variation (CV) of the Shannon diversity index (SDI) and unweighted and weighted UniFrac distances per patient, per site. Measurements of intra-patient temporal variability and patient stability categories were analyzed for their correlations with genera abundances. Groups of patients were analyzed to determine if patients with adverse outcomes had significantly different levels of microbiome temporal variability. Potential clinical drivers of microbiome temporal instability were determined using multivariable regression analyses. RESULTS Our cohort evidenced a high degree of intra-patient temporal instability of stool and oral microbial diversity based on SDI CV. We identified statistically significant differences in the relative abundance of multiple taxa amongst individuals with different levels of microbiota temporal stability. Increased intra-patient temporal variability of the oral SDI was correlated with increased risk of infection during IC (P = 0.02), and higher stool SDI CVs were correlated with increased risk of infection 90 days post-IC (P = 0.04). Total days on antibiotics was significantly associated with increased temporal variability of both oral microbial diversity (P = 0.03) and community structure (P = 0.002). CONCLUSIONS These data quantify the longitudinal variability of the oral and gut microbiota in AML patients, show that increased variability was correlated with adverse clinical outcomes, and offer the possibility of using stabilizing taxa as a method of focused microbiome repletion. Furthermore, these results support the importance of longitudinal microbiome sampling and analyses, rather than one time measurements, in research and future clinical practice.
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Affiliation(s)
- Jessica R Galloway-Peña
- Department of Infectious Disease, Infection Control and Employee Health, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Daniel P Smith
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pranoti Sahasrabhojane
- Department of Infectious Disease, Infection Control and Employee Health, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - Bryan M Fellman
- Department of Biostatistics, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Nadim J Ajami
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Naval Daver
- Department of Leukemia, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Michele Guindani
- Department of Statistics, University of California, Irvine, CA, 92697, USA
| | - Joseph F Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dimitrios P Kontoyiannis
- Department of Infectious Disease, Infection Control and Employee Health, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Samuel A Shelburne
- Department of Infectious Disease, Infection Control and Employee Health, MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Woodworth MH, Carpentieri C, Sitchenko KL, Kraft CS. Challenges in fecal donor selection and screening for fecal microbiota transplantation: A review. Gut Microbes 2017; 8:225-237. [PMID: 28129018 PMCID: PMC5479407 DOI: 10.1080/19490976.2017.1286006] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Fecal microbiota transplantation is best understood as an effective and inexpensive therapy for recurrent Clostridium difficile infection but fecal donor selection and screening should be periodically revised. Here, we review current recommendations for selection and screening of fecal donors for fecal microbiota transplantation. We recommend considering diabetes mellitus, prior cardiovascular events, and clinical healthcare exposure as fecal donor exclusion criteria until more is known about the association of these conditions with the human gut microbiome. We review the non-bacterial members of the human gut microbiome, associations of the gut microbiome with colorectal malignancies, the human gut resistome and how these may impact future donor screening recommendations. Collaboration between clinicians, clinical laboratory scientists, industry and regulatory agencies will be critically important for continued improvement in donor selection and screening.
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Affiliation(s)
- Michael H. Woodworth
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Cynthia Carpentieri
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Kaitlin L. Sitchenko
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Colleen S. Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA,Department of Pathology, Emory University Hospital, Atlanta, GA, USA,CONTACT Colleen S. Kraft Division of Infectious Diseases, Department of Pathology, Emory University Hospital, 1364 Clifton Rd., NE, Suite F145C, Atlanta, GA 30322, USA
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Araos R, Tai AK, Snyder GM, Blaser MJ, D'Agata EMC. Predominance of Lactobacillus spp. Among Patients Who Do Not Acquire Multidrug-Resistant Organisms. Clin Infect Dis 2016; 63:937-943. [PMID: 27358350 DOI: 10.1093/cid/ciw426] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/17/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The emergence and dissemination of multidrug-resistant organisms (MDROs) is a global threat. Characterizing the human microbiome among hospitalized patients and identifying unique microbial signatures among those patients who acquire MDROs may identify novel infection prevention strategies. METHODS Adult patients admitted to 5 general medical-surgical floors at a 649-bed, tertiary care center in Boston, Massachusetts, were classified according to in-hospital antimicrobial exposure and MDRO colonization status. Within 48 hours of hospital admission (baseline) and at discharge (follow-up), rectal swab samples were obtained, and compared with samples from an external control group of healthy persons from the community. DNA was extracted from samples, next-generation sequencing performed, and microbial community structure and taxonomic features assessed, comparing those who acquired MDROs and those who had not, and the external controls. RESULTS Hospitalized patients (n = 44) had reduced microbial diversity and a greater abundance of Escherichia spp. and Enterococcus spp. than healthy controls (n = 26). Among hospitalized patients, 25 had no MDROs at the time of the baseline sample and were also exposed to antimicrobials. Among this group, 7 (28%) acquired ≥1 MDRO; demographic and clinical characteristics were similar between MDRO-acquisition and MDRO-nonacquisition groups. Patients in the nonacquisition group had consistently higher Lactobacillus spp. abundance than those in the acquisition group (linear discriminant score, 3.97; P = .04). CONCLUSIONS The fecal microbiota of the hospitalized subjects had abnormal community composition, and Lactobacillus spp. was associated with lack of MDRO acquisition, consistent with a protective role.
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Affiliation(s)
- Rafael Araos
- Department of Medicine, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Albert K Tai
- Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine
| | - Graham M Snyder
- Department of Medicine, Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, Massachusetts
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