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Maffioli EM, Montás MC, Anyakora C. Excessive active pharmaceutical ingredients in substandard and falsified drugs should also raise concerns in low-income countries. J Glob Health 2024; 14:03029. [PMID: 38843042 PMCID: PMC11156249 DOI: 10.7189/jogh.14.03029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024] Open
Affiliation(s)
- Elisa M Maffioli
- University of Michigan, School of Public Health, Department of Health Management and Policy, Ann Arbor, Michigan, USA
| | - Marie C Montás
- Harvard T. H. Chan School of Public Health, Department of Global Health and Population, Boston, Massachusetts, USA
| | - Chimezie Anyakora
- Bloom Public Health, Abuja, Nigeria
- School of Science and Technology, Pan Atlantic University, Lagos, Nigeria
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2
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Lamichhane J, Choi BI, Stegman N, Fontes Noronha M, Wolfe AJ. Macrolide Resistance in the Aerococcus urinae Complex: Implications for Integrative and Conjugative Elements. Antibiotics (Basel) 2024; 13:433. [PMID: 38786161 PMCID: PMC11117264 DOI: 10.3390/antibiotics13050433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The recognition of the Aerococcus urinae complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic resistance profiles. Here, we investigated the prevalence of macrolide resistance within urinary AUC isolates, shedding light on potential genetic mechanisms. Phenotypic testing revealed a high rate of macrolide resistance: 45%, among a total of 189 urinary AUC isolates. Genomic analysis identified integrative and conjugative elements (ICEs) as carriers of the macrolide resistance gene ermA, suggesting horizontal gene transfer as a mechanism of resistance. Furthermore, comparison with publicly available genomes of related pathogens revealed high ICE sequence homogeneity, highlighting the potential for cross-species dissemination of resistance determinants. Understanding mechanisms of resistance is crucial for developing effective surveillance strategies and improving antibiotic use. Furthermore, the findings underscore the importance of considering the broader ecological context of resistance dissemination, emphasizing the need for community-level surveillance to combat the spread of antibiotic resistance within the urinary microbiome.
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Affiliation(s)
- Jyoti Lamichhane
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA (M.F.N.)
| | - Brian I. Choi
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA (M.F.N.)
| | - Natalie Stegman
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA;
| | - Melline Fontes Noronha
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA (M.F.N.)
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA (M.F.N.)
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3
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Roa-Tort K, Saavedra Y, Villanueva-Martínez A, Ganem-Rondero A, Pérez-Carranza LA, de la Rosa-Vázquez JM, Ugalde-Femat G, Molina-Alejandre O, Becerril-Osnaya AA, Rivera-Fernández JD. In Vitro Antimicrobial Photodynamic Therapy for Pseudomonas aeruginosa ( P. aeruginosa) and methicillin-resistant Staphylococcus aureus (MRSA) Inhibition Using a Green Light Source. Pharmaceutics 2024; 16:518. [PMID: 38675180 PMCID: PMC11053950 DOI: 10.3390/pharmaceutics16040518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Photodynamic therapy (PDT) has been based on using photosensitizers (PS) and applying light of a specific wavelength. When this technique is used for treating infections, it is known as antimicrobial photodynamic therapy (aPDT). Currently, the use of lighting sources for in vitro studies using aPDT is generally applied in multiwell cell culture plates; however, depending on the lighting arrangement, there are usually errors in the application of the technique because the light from a well can affect the neighboring wells or it may be that not all the wells are used in the same experiment. In addition, one must be awarded high irradiance values, which can cause unwanted photothermal problems in the studies. Thus, this manuscript presents an in vitro antimicrobial photodynamic therapy for a Pseudomonas aeruginosa (P. aeruginosa) and methicillin-resistant Staphylococcus aureus (MRSA) inhibition study using an arrangement of thermally isolated and independently illuminated green light source systems for eight tubes in vitro aPDT, determining the effect of the following factors: (i) irradiance level, (ii) exposure time, and (iii) Rose Bengal (RB) concentration (used as a PS), registering the Pseudomonas aeruginosa (P. aeruginosa) and methicillin-resistant Staphylococcus aureus (MRSA) inhibition rates. The results show that in the dark, RB had a poor antimicrobial rate for P. aeruginosa, finding the maximum inhibition (2.7%) at 30 min with an RB concentration of 3 µg/mL. However, by applying light in a correct dosage (time × irradiance) and the adequate RB concentration, the inhibition rate increased by over 37%. In the case of MRSA, there was no significant inhibition with RB in complete darkness and, in contrast, the rate was 100% for those experiments that were irradiated.
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Affiliation(s)
- Karen Roa-Tort
- Laboratorio de Optomecatrónica, UPIIH, Instituto Politécnico Nacional, Distrito de Educación, Salud, Ciencia, Tecnología e Innovación, San Agustín Tlaxiaca 42162, Mexico;
| | - Yael Saavedra
- Laboratorio de Biofotónica, ESIME ZAC, Instituto Politécnico Nacional, Gustavo A. Madero, Ciudad de México 07738, Mexico; (Y.S.); (J.M.d.l.R.-V.); (G.U.-F.)
| | - Angélica Villanueva-Martínez
- Laboratorio de Investigación y Posgrado en Tecnología Farmacéutica (L-322), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli 54740, Mexico; (A.V.-M.); (A.G.-R.); (O.M.-A.)
| | - Adriana Ganem-Rondero
- Laboratorio de Investigación y Posgrado en Tecnología Farmacéutica (L-322), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli 54740, Mexico; (A.V.-M.); (A.G.-R.); (O.M.-A.)
| | - Laura Abril Pérez-Carranza
- Laboratorio de Bacteriología Diagnóstica de la Sección de Ciencias de la Salud Humana (anexo al L-513, Campo1), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli 54740, Mexico;
| | - José M. de la Rosa-Vázquez
- Laboratorio de Biofotónica, ESIME ZAC, Instituto Politécnico Nacional, Gustavo A. Madero, Ciudad de México 07738, Mexico; (Y.S.); (J.M.d.l.R.-V.); (G.U.-F.)
| | - Gabriel Ugalde-Femat
- Laboratorio de Biofotónica, ESIME ZAC, Instituto Politécnico Nacional, Gustavo A. Madero, Ciudad de México 07738, Mexico; (Y.S.); (J.M.d.l.R.-V.); (G.U.-F.)
| | - Omar Molina-Alejandre
- Laboratorio de Investigación y Posgrado en Tecnología Farmacéutica (L-322), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli 54740, Mexico; (A.V.-M.); (A.G.-R.); (O.M.-A.)
| | - Andrea Angela Becerril-Osnaya
- Laboratorio de Bacteriología Diagnóstica de la Sección de Ciencias de la Salud Humana (anexo al L-513, Campo1), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli 54740, Mexico;
| | - Josué D. Rivera-Fernández
- Laboratorio de Optomecatrónica, UPIIH, Instituto Politécnico Nacional, Distrito de Educación, Salud, Ciencia, Tecnología e Innovación, San Agustín Tlaxiaca 42162, Mexico;
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Brar NK, Dhariwal A, Åmdal HA, Junges R, Salvadori G, Baker JL, Edlund A, Petersen FC. Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome. NPJ Biofilms Microbiomes 2024; 10:37. [PMID: 38565843 PMCID: PMC10987642 DOI: 10.1038/s41522-024-00507-7] [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: 08/28/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Prolonged exposure to antibiotics at low concentration can promote processes associated with bacterial biofilm formation, virulence and antibiotic resistance. This can be of high relevance in microbial communities like the oral microbiome, where commensals and pathogens share a common habitat and where the total abundance of antibiotic resistance genes surpasses the abundance in the gut. Here, we used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability. The ecological impact on the microbiome and resistome was investigated using shotgun metagenomics. The results showed that low concentrations promoted significant shifts in microbial taxonomic profile and could enhance biofilm viability by up to 1 to 2-log. For the resistome, low concentrations had no significant impact on antibiotic resistance gene (ARG) diversity, while ARG abundance decreased by up to 84%. A positive correlation was observed between reduced microbial diversity and reduced ARG abundance. The WHO priority pathogens Streptococcus pneumoniae and Staphylococcus aureus were identified in some of the samples, but their abundance was not significantly altered by ampicillin. Most of the antibiotic resistance genes that increased in abundance in the ampicillin group were associated with streptococci, including Streptococcus mitis, a well-known potential donor of ARGs to S. pneumoniae. Overall, the results highlight the potential of using the model to further our understanding of ecological and evolutionary forces driving antimicrobial resistance in oral microbiomes.
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Affiliation(s)
- N K Brar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - A Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - H A Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - R Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - G Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - J L Baker
- Department of Oral Rehabilitation & Biosciences, Oregon Health & Science University, Portland, OR, USA
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA, USA
| | - A Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA, USA
| | - F C Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway.
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Dornelas-Figueira LM, Ricomini Filho AP, Junges R, Åmdal HA, Cury AADB, Petersen FC. In Vitro Impact of Fluconazole on Oral Microbial Communities, Bacterial Growth, and Biofilm Formation. Antibiotics (Basel) 2023; 12:1433. [PMID: 37760729 PMCID: PMC10525723 DOI: 10.3390/antibiotics12091433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/30/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Antifungal agents are widely used to specifically eliminate infections by fungal pathogens. However, the specificity of antifungal agents has been challenged by a few studies demonstrating antibacterial inhibitory effects against Mycobacteria and Streptomyces species. Here, we evaluated for the first time the potential effect of fluconazole, the most clinically used antifungal agent, on a human oral microbiota biofilm model. The results showed that biofilm viability on blood and mitis salivarius agar media was increased over time in the presence of fluconazole at clinically relevant concentrations, despite a reduction in biomass. Targeted PCR revealed a higher abundance of Veillonella atypica, Veillonella dispar, and Lactobacillus spp. in the fluconazole-treated samples compared to the control, while Fusobacterium nucleatum was reduced and Streptococcus spp were not significantly affected. Further, we tested the potential impact of fluconazole using single-species models. Our results, using Streptococcus mutans and Streptococcus mitis luciferase reporters, showed that S. mutans planktonic growth was not significantly affected by fluconazole, whereas for S. mitis, planktonic growth, but not biofilm viability, was inhibited at the highest concentration. Fluconazole's effects on S. mitis biofilm biomass were concentration and time dependent. Exposure for 48 h to the highest concentration of fluconazole was associated with S. mitis biofilms with the most increased biomass. Potential growth inhibitory effects were further tested using four non-streptococcal species. Among these, the planktonic growth of both Escherichia coli and Granulicatella adiacens was inhibited by fluconazole. The data indicate bacterial responses to fluconazole that extend to a broader range of bacterial species than previously anticipated from the literature, with the potential to disturb biofilm communities.
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Affiliation(s)
- Louise Morais Dornelas-Figueira
- Department of Prosthodontics and Periodontology, Piracicaba Dental School, University of Campinas, Piracicaba 13414-903, SP, Brazil
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
| | - Antônio Pedro Ricomini Filho
- Department of Physiological Sciences, Piracicaba Dental School, University of Campinas, Piracicaba 13414-903, SP, Brazil
| | - Roger Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
| | - Heidi Aarø Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
| | - Altair Antoninha Del Bel Cury
- Department of Prosthodontics and Periodontology, Piracicaba Dental School, University of Campinas, Piracicaba 13414-903, SP, Brazil
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Aricò MO, Valletta E, Caselli D. Appropriate Use of Antibiotic and Principles of Antimicrobial Stewardship in Children. CHILDREN (BASEL, SWITZERLAND) 2023; 10:740. [PMID: 37189989 PMCID: PMC10137055 DOI: 10.3390/children10040740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023]
Abstract
Antibiotics account for over 10% of the overall drug expense of the National Health System in Italy in 2021. Their use in children is of particular interest on one side, because acute infections are very common in children, while they build their immunologic library of competence; on the other side, although many acute infections are expected and turn out to be of viral origin, caregivers will often ask the family doctor or primary care attending to reassure them by prescribing antibiotic treatment, although it may often be unnecessary. The inappropriate prescription of antibiotics in children may likely be a source not only of undue economic burden for the public health system but also of increasing development of antimicrobial resistance (AMR). Based on those issues, the inappropriate use of antibiotics in children should be avoided to reduce the risks of unnecessary toxicity, increase in health costs, lifelong effects, and selection of resistant organisms causing undue deaths. Antimicrobial stewardship (AMS) describes a coherent set of actions that ensure an optimal use of antimicrobials to improve patient outcomes while limiting the risk of adverse events including AMR. The aim of this paper is to spread some concept of good use of antibiotics for pediatricians or every other physician involved in the choice to prescribe, or not, antibiotics in children. Several actions could be of help in this process, including the following: (1) identify patients with high probability of bacterial infection; (2) collect samples for culture study before starting antibiotic treatment if invasive bacterial infection is suspected; (3) select the appropriate antibiotic molecule based on local resistance and narrow spectrum for the suspected pathogen(s); avoid multi-antibiotic association; prescribe correct dosage; (4) choose the best route of administration (oral vs. parenteral) and the best schedule of administration for every prescription (i.e., multiple administration for beta lactam); (5) schedule clinical and laboratory re-evaluation with the aim to consider therapeutic de-escalation; (6) stop antibiotic administration as soon as possible, avoiding the application of "antibiotic course".
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Affiliation(s)
- Melodie O. Aricò
- U.O. Pediatria, Ospedale G.B. Morgagni—L. Pierantoni, AUSL Romagna, 47121 Forlì, Italy; (M.O.A.); (E.V.)
| | - Enrico Valletta
- U.O. Pediatria, Ospedale G.B. Morgagni—L. Pierantoni, AUSL Romagna, 47121 Forlì, Italy; (M.O.A.); (E.V.)
| | - Désirée Caselli
- U.O.C. Malattie Infettive, Ospedale Pediatrico Giovanni XXIII, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70100 Bari, Italy
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Coque TM, Cantón R, Pérez-Cobas AE, Fernández-de-Bobadilla MD, Baquero F. Antimicrobial Resistance in the Global Health Network: Known Unknowns and Challenges for Efficient Responses in the 21st Century. Microorganisms 2023; 11:1050. [PMID: 37110473 PMCID: PMC10144039 DOI: 10.3390/microorganisms11041050] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the Global Health challenges of the 21st century. The inclusion of AMR on the global map parallels the scientific, technological, and organizational progress of the healthcare system and the socioeconomic changes of the last 100 years. Available knowledge about AMR has mostly come from large healthcare institutions in high-income countries and is scattered in studies across various fields, focused on patient safety (infectious diseases), transmission pathways and pathogen reservoirs (molecular epidemiology), the extent of the problem at a population level (public health), their management and cost (health economics), cultural issues (community psychology), and events associated with historical periods (history of science). However, there is little dialogue between the aspects that facilitate the development, spread, and evolution of AMR and various stakeholders (patients, clinicians, public health professionals, scientists, economic sectors, and funding agencies). This study consists of four complementary sections. The first reviews the socioeconomic factors that have contributed to building the current Global Healthcare system, the scientific framework in which AMR has traditionally been approached in such a system, and the novel scientific and organizational challenges of approaching AMR in the fourth globalization scenario. The second discusses the need to reframe AMR in the current public health and global health contexts. Given that the implementation of policies and guidelines are greatly influenced by AMR information from surveillance systems, in the third section, we review the unit of analysis ("the what" and "the who") and the indicators (the "operational units of surveillance") used in AMR and discuss the factors that affect the validity, reliability, and comparability of the information to be applied in various healthcare (primary, secondary, and tertiary), demographic, and economic contexts (local, regional, global, and inter-sectorial levels). Finally, we discuss the disparities and similarities between distinct stakeholders' objectives and the gaps and challenges of combatting AMR at various levels. In summary, this is a comprehensive but not exhaustive revision of the known unknowns about how to analyze the heterogeneities of hosts, microbes, and hospital patches, the role of surrounding ecosystems, and the challenges they represent for surveillance, antimicrobial stewardship, and infection control programs, which are the traditional cornerstones for controlling AMR in human health.
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Affiliation(s)
- Teresa M. Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana Elena Pérez-Cobas
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Miguel D. Fernández-de-Bobadilla
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Pei S, Blumberg S, Vega JC, Robin T, Zhang Y, Medford RJ, Adhikari B, Shaman J. Challenges in Forecasting Antimicrobial Resistance. Emerg Infect Dis 2023; 29:679-685. [PMID: 36958029 PMCID: PMC10045679 DOI: 10.3201/eid2904.221552] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023] Open
Abstract
Antimicrobial resistance is a major threat to human health. Since the 2000s, computational tools for predicting infectious diseases have been greatly advanced; however, efforts to develop real-time forecasting models for antimicrobial-resistant organisms (AMROs) have been absent. In this perspective, we discuss the utility of AMRO forecasting at different scales, highlight the challenges in this field, and suggest future research priorities. We also discuss challenges in scientific understanding, access to high-quality data, model calibration, and implementation and evaluation of forecasting models. We further highlight the need to initiate research on AMRO forecasting using currently available data and resources to galvanize the research community and address initial practical questions.
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Wollein Waldetoft K, Sundius S, Kuske R, Brown SP. Defining the Benefits of Antibiotic Resistance in Commensals and the Scope for Resistance Optimization. mBio 2023; 14:e0134922. [PMID: 36475750 PMCID: PMC9972992 DOI: 10.1128/mbio.01349-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance is a major medical and public health challenge, characterized by global increases in the prevalence of resistant strains. The conventional view is that all antibiotic resistance is problematic, even when not in pathogens. Resistance in commensal bacteria poses risks, as resistant organisms can provide a reservoir of resistance genes that can be horizontally transferred to pathogens or may themselves cause opportunistic infections in the future. While these risks are real, we propose that commensal resistance can also generate benefits during antibiotic treatment of human infection, by promoting continued ecological suppression of pathogens. To define and illustrate this alternative conceptual perspective, we use a two-species mathematical model to identify the necessary and sufficient ecological conditions for beneficial resistance. We show that the benefits are limited to species (or strain) interactions where commensals suppress pathogen growth and are maximized when commensals compete with, rather than prey on or otherwise exploit pathogens. By identifying benefits of commensal resistance, we propose that rather than strictly minimizing all resistance, resistance management may be better viewed as an optimization problem. We discuss implications in two applied contexts: bystander (nontarget) selection within commensal microbiomes and pathogen treatment given polymicrobial infections. IMPORTANCE Antibiotic resistance is commonly viewed as universally costly, regardless of which bacterial cells express resistance. Here, we derive an opposing logic, where resistance in commensal bacteria can lead to reductions in pathogen density and improved outcomes on both the patient and public health scales. We use a mathematical model of commensal-pathogen interactions to define the necessary and sufficient conditions for beneficial resistance, highlighting the importance of reciprocal ecological inhibition to maximize the benefits of resistance. More broadly, we argue that determining the benefits as well as the costs of resistances in human microbiomes can transform resistance management from a minimization to an optimization problem. We discuss applied contexts and close with a review of key resistance optimization dimensions, including the magnitude, spectrum, and mechanism of resistance.
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Affiliation(s)
- Kristofer Wollein Waldetoft
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Torsby Hospital, Torsby, Sweden
| | - Sarah Sundius
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Mathematics, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rachel Kuske
- School of Mathematics, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sam P. Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
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Natterson-Horowitz B, Aktipis A, Fox M, Gluckman PD, Low FM, Mace R, Read A, Turner PE, Blumstein DT. The future of evolutionary medicine: sparking innovation in biomedicine and public health. FRONTIERS IN SCIENCE 2023; 1:997136. [PMID: 37869257 PMCID: PMC10590274 DOI: 10.3389/fsci.2023.997136] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Evolutionary medicine - i.e. the application of insights from evolution and ecology to biomedicine - has tremendous untapped potential to spark transformational innovation in biomedical research, clinical care and public health. Fundamentally, a systematic mapping across the full diversity of life is required to identify animal model systems for disease vulnerability, resistance, and counter-resistance that could lead to novel clinical treatments. Evolutionary dynamics should guide novel therapeutic approaches that target the development of treatment resistance in cancers (e.g., via adaptive or extinction therapy) and antimicrobial resistance (e.g., via innovations in chemistry, antimicrobial usage, and phage therapy). With respect to public health, the insight that many modern human pathologies (e.g., obesity) result from mismatches between the ecologies in which we evolved and our modern environments has important implications for disease prevention. Life-history evolution can also shed important light on patterns of disease burden, for example in reproductive health. Experience during the COVID-19 (SARS-CoV-2) pandemic has underlined the critical role of evolutionary dynamics (e.g., with respect to virulence and transmissibility) in predicting and managing this and future pandemics, and in using evolutionary principles to understand and address aspects of human behavior that impede biomedical innovation and public health (e.g., unhealthy behaviors and vaccine hesitancy). In conclusion, greater interdisciplinary collaboration is vital to systematically leverage the insight-generating power of evolutionary medicine to better understand, prevent, and treat existing and emerging threats to human, animal, and planetary health.
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Affiliation(s)
- B. Natterson-Horowitz
- Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Athena Aktipis
- Department of Psychology, Arizona State University, Tempe, AZ, United States
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, United States
| | - Molly Fox
- Department of Anthropology, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, United States
| | - Peter D. Gluckman
- Koi Tū: The Centre for Informed Futures, University of Auckland, Auckland, New Zealand
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Felicia M. Low
- Koi Tū: The Centre for Informed Futures, University of Auckland, Auckland, New Zealand
| | - Ruth Mace
- Department of Anthropology, University College London, London, United Kingdom
| | - Andrew Read
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, State College, PA, United States
- Department of Entomology, The Pennsylvania State University, State College, PA, United States
- Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA, United States
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
- Program in Microbiology, Yale School of Medicine, New Haven, CT, United States
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
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Rajar P, Dhariwal A, Salvadori G, Junges R, Åmdal HA, Berild D, Fugelseth D, Saugstad OD, Lausten-Thomsen U, Greisen G, Haaland K, Petersen FC. Microbial DNA extraction of high-host content and low biomass samples: Optimized protocol for nasopharynx metagenomic studies. Front Microbiol 2022; 13:1038120. [PMID: 36620054 PMCID: PMC9811202 DOI: 10.3389/fmicb.2022.1038120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Low microbial biomass and high human DNA content in nasopharyngeal aspirate samples hinder comprehensive characterization of microbiota and resistome. We obtained samples from premature infants, a group with increased risk of developing respiratory disorders and infections, and consequently frequent exposure to antibiotics. Our aim was to devise an optimal protocol for handling nasopharyngeal aspirate samples from premature infants, focusing on host DNA depletion and microbiome and resistome characterization. Methods Three depletion and three DNA extraction protocols were compared, using RT-PCR and whole metagenome sequencing to determine the efficiency of human DNA removal, taxonomic profiling and assignment of antibiotic resistance genes. Protocols were tested using mock communities, as well as pooled and individual patient samples. Results The only extraction protocol to retrieve the expected DNA yield from mock community samples was based on a lytic method to improve Gram positive recovery (MasterPure™). Host DNA content in non-depleted aliquots from pooled patient samples was 99%. Only samples depleted with MolYsis™ showed satisfactory, but varied reduction in host DNA content, in both pooled and individual patient samples, allowing for microbiome and resistome characterisation (host DNA content from 15% to 98%). Other depletion protocols either retrieved too low total DNA yields, preventing further analysis, or failed to reduce host DNA content. By using Mol_MasterPure protocol on aliquots from pooled patient samples, we increased the number of bacterial reads by 7.6 to 1,725.8-fold compared to non-depleted reference samples. PCR results were indicative of achieved microbial enrichment. Individual patient samples processed with Mol_MasterPure protocol varied greatly in total DNA yield, host DNA content (from 40% to 98%), species and antibiotic resistance gene richness. Discussion Despite high human DNA and low microbial biomass content in nasopharynx aspirates of preterm infants, we were able to reduce host DNA content to levels compatible with downstream shotgun metagenomic analysis, including bacterial species identification and coverage of antibiotic resistance genes. Whole metagenomic sequencing of microbes colonizing the nasopharynx may contribute to explaining the possible role of airway microbiota in respiratory conditions and reveal carriage of antibiotic resistance genes.
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Affiliation(s)
- Polona Rajar
- Department of Neonatal Intensive Care, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Ullevål, Oslo, Norway,Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Achal Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Gabriela Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Roger Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Heidi Aarø Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Dag Berild
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, Oslo University, Oslo, Norway
| | - Drude Fugelseth
- Department of Neonatal Intensive Care, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Ullevål, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, Oslo University, Oslo, Norway
| | | | - Ulrik Lausten-Thomsen
- Department of Neonatology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Gorm Greisen
- Department of Neonatology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kirsti Haaland
- Department of Neonatal Intensive Care, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Ullevål, Oslo, Norway
| | - Fernanda Cristina Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway,*Correspondence: Fernanda Cristina Petersen,
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12
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Lebeaux RM, Madan JC, Nguyen QP, Coker MO, Dade EF, Moroishi Y, Palys TJ, Ross BD, Pettigrew MM, Morrison HG, Karagas MR, Hoen AG. Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies. Pediatr Res 2022; 92:1757-1766. [PMID: 35568730 PMCID: PMC9659678 DOI: 10.1038/s41390-022-02104-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/04/2022] [Accepted: 03/29/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Young children are frequently exposed to antibiotics, with the potential for collateral consequences to the gut microbiome. The impact of antibiotic exposures to off-target microbes (i.e., bacteria not targeted by treatment) and antibiotic resistance genes (ARGs) is poorly understood. METHODS We used metagenomic sequencing data from paired stool samples collected prior to antibiotic exposure and at 1 year from over 200 infants and a difference-in-differences approach to assess the relationship between subsequent exposures and the abundance or compositional diversity of microbes and ARGs while adjusting for covariates. RESULTS By 1 year, the abundance of multiple species and ARGs differed by antibiotic exposure. Compared to infants never exposed to antibiotics, Bacteroides vulgatus relative abundance increased by 1.72% (95% CI: 0.19, 3.24) while Bacteroides fragilis decreased by 1.56% (95% CI: -4.32, 1.21). Bifidobacterium species also exhibited opposing trends. ARGs associated with exposure included class A beta-lactamase gene CfxA6. Among infants attending day care, Escherichia coli and ARG abundance were both positively associated with antibiotic use. CONCLUSION Novel findings, including the importance of day care attendance, were identified through considering microbiome data at baseline and post-intervention. Thus, our study design and approach have important implications for future studies evaluating the unintended impacts of antibiotics. IMPACT The impact of antibiotic exposure to off-target microbes and antibiotic resistance genes in the gut is poorly defined. We quantified these impacts in two cohort studies using a difference-in-differences approach. Novel to microbiome studies, we used pre/post-antibiotic data to emulate a randomized controlled trial. Compared to infants unexposed to antibiotics between baseline and 1 year, the relative abundance of multiple off-target species and antibiotic resistance genes was altered. Infants who attended day care and were exposed to antibiotics within the first year had a higher abundance of Escherichia coli and antibiotic resistance genes; a novel finding warranting further investigation.
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Affiliation(s)
- Rebecca M Lebeaux
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Juliette C Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Pediatrics, Children's Hospital at Dartmouth, Lebanon, NH, USA
- Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Quang P Nguyen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Modupe O Coker
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Erika F Dade
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Yuka Moroishi
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Thomas J Palys
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Benjamin D Ross
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Orthopaedics, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Melinda M Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
- Center for Molecular Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Anne G Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
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13
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Kittiwan N, Calland JK, Mourkas E, Hitchings MD, Murray S, Tadee P, Tadee P, Duangsonk K, Meric G, Sheppard SK, Patchanee P, Pascoe B. Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs. Microb Genom 2022; 8:mgen000882. [PMID: 36326658 PMCID: PMC9836093 DOI: 10.1099/mgen.0.000882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Streptococcus suis is a leading cause of bacterial meningitis in South-East Asia, with frequent zoonotic transfer to humans associated with close contact with pigs. A small number of invasive lineages are responsible for endemic infection in the swine industry, causing considerable global economic losses. A lack of surveillance and a rising trend in clinical treatment failure has raised concerns of growing antimicrobial resistance (AMR) among invasive S. suis. Gene flow between healthy and disease isolates is poorly understood and, in this study, we sample and sequence a collection of isolates predominantly from healthy pigs in Chiang Mai province, Northern Thailand. Pangenome characterization identified extensive genetic diversity and frequent AMR carriage in isolates from healthy pigs. Multiple AMR genes were identified, conferring resistance to aminoglycosides, lincosamides, tetracycline and macrolides. All isolates were non-susceptible to three or more different antimicrobial classes, and 75 % of non-serotype 2 isolates were non-susceptible to six or more classes (compared to 37.5 % of serotype 2 isolates). AMR genes were found on integrative and conjugative elements previously observed in other species, suggesting a mobile gene pool that can be accessed by invasive disease isolates. This article contains data hosted by Microreact.
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Affiliation(s)
- Nattinee Kittiwan
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Veterinary Research and Development Center (Upper Northern Region), Hang Chat, Lampang 52190, Thailand
| | - Jessica K. Calland
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Evangelos Mourkas
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK
| | - Matthew D. Hitchings
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, UK
| | - Susan Murray
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, UK,Present address: Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, UK
| | - Pakpoom Tadee
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Phacharaporn Tadee
- Faculty of Animal Science and Technology, Maejo University, Chiang Mai 50290, Thailand
| | - Kwanjit Duangsonk
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Guillaume Meric
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK,Present address: Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Samuel K. Sheppard
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK,Faculty of Allied Medical Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Prapas Patchanee
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,*Correspondence: Prapas Patchanee,
| | - Ben Pascoe
- Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK,Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK,*Correspondence: Ben Pascoe,
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14
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Enterotoxin tilimycin from gut-resident Klebsiella promotes mutational evolution and antibiotic resistance in mice. Nat Microbiol 2022; 7:1834-1848. [PMID: 36289400 PMCID: PMC9613472 DOI: 10.1038/s41564-022-01260-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022]
Abstract
Klebsiella spp. that secrete the DNA-alkylating enterotoxin tilimycin colonize the human intestinal tract. Numbers of toxigenic bacteria increase during antibiotic use, and the resulting accumulation of tilimycin in the intestinal lumen damages the epithelium via genetic instability and apoptosis. Here we examine the impact of this genotoxin on the gut ecosystem. 16S rRNA sequencing of faecal samples from mice colonized with Klebsiella oxytoca strains and mechanistic analyses show that tilimycin is a pro-mutagenic antibiotic affecting multiple phyla. Transient synthesis of tilimycin in the murine gut antagonized niche competitors, reduced microbial richness and altered taxonomic composition of the microbiota both during and following exposure. Moreover, tilimycin secretion increased rates of mutagenesis in co-resident opportunistic pathogens such as Klebsiella pneumoniae and Escherichia coli, as shown by de novo acquisition of antibiotic resistance. We conclude that tilimycin is a bacterial mutagen, and flares of genotoxic Klebsiella have the potential to drive the emergence of resistance, destabilize the gut microbiota and shape its evolutionary trajectory. Production of the enterotoxin tilimycin by gut-resident Klebsiella species can alter gut microbiota composition, induce mutational evolution and drive the emergence of antibiotic resistance in mice.
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15
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Agyeman WY, Bisht A, Gopinath A, Cheema AH, Chaludiya K, Khalid M, Nwosu M, Konka S, Khan S. A Systematic Review of Antibiotic Resistance Trends and Treatment Options for Hospital-Acquired Multidrug-Resistant Infections. Cureus 2022; 14:e29956. [PMID: 36381838 PMCID: PMC9635809 DOI: 10.7759/cureus.29956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022] Open
Abstract
Antimicrobial resistance is a major public health challenge described by the World Health Organization as one of the top 10 public health challenges worldwide. Drug-resistant microbes contribute significantly to morbidity and mortality in the hospital, especially in the critical care unit. The primary etiology of increasing antibiotic resistance is inappropriate and excessive use of antibiotics. The alarming rise of drug-resistant microbes worldwide threatens to erode our ability to treat infections with our current armamentarium of antibiotics. Unfortunately, the pace of development of new antibiotics by the pharmaceutical industry has not kept up with rising resistance to expand our options to treat microbial infections. The costs of antibiotic resistance include death and disability, extended hospital stays due to prolonged sickness, need for expensive therapies, rising healthcare expenditure, reduced productivity from time out of the workforce, and rising penury. This review sums up the common mechanisms, trends, and treatment options for hospital-acquired multidrug-resistant microbes.
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16
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Rogawski McQuade ET, Brennhofer SA, Elwood SE, McMurry TL, Lewnard JA, Mduma ER, Shrestha S, Iqbal N, Bessong PO, Kang G, Kosek M, Lima AAM, Ahmed T, Liu J, Houpt ER, Platts-Mills JA. Frequency of bystander exposure to antibiotics for enteropathogenic bacteria among young children in low-resource settings. Proc Natl Acad Sci U S A 2022; 119:e2208972119. [PMID: 36037372 PMCID: PMC9457395 DOI: 10.1073/pnas.2208972119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 11/24/2022] Open
Abstract
Children in low-resource settings carry enteric pathogens asymptomatically and are frequently treated with antibiotics, resulting in opportunities for pathogens to be exposed to antibiotics when not the target of treatment (i.e., bystander exposure). We quantified the frequency of bystander antibiotic exposures for enteric pathogens and estimated associations with resistance among children in eight low-resource settings. We analyzed 15,697 antibiotic courses from 1,715 children aged 0 to 2 y from the MAL-ED birth cohort. We calculated the incidence of bystander exposures and attributed exposures to respiratory and diarrheal illnesses. We associated bystander exposure with phenotypic susceptibility of E. coli isolates in the 30 d following exposure and at the level of the study site. There were 744.1 subclinical pathogen exposures to antibiotics per 100 child-years. Enteroaggregative Escherichia coli was the most frequently exposed pathogen, with 229.6 exposures per 100 child-years. Almost all antibiotic exposures for Campylobacter (98.8%), enterotoxigenic E. coli (95.6%), and typical enteropathogenic E. coli (99.4%), and the majority for Shigella (77.6%), occurred when the pathogens were not the target of treatment. Respiratory infections accounted for half (49.9%) and diarrheal illnesses accounted for one-fourth (24.6%) of subclinical enteric bacteria exposures to antibiotics. Bystander exposure of E. coli to class-specific antibiotics was associated with the prevalence of phenotypic resistance at the community level. Antimicrobial stewardship and illness-prevention interventions among children in low-resource settings would have a large ancillary benefit of reducing bystander selection that may contribute to antimicrobial resistance.
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Affiliation(s)
| | - Stephanie A. Brennhofer
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA 22908
| | - Sarah E. Elwood
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA 22908
| | - Timothy L. McMurry
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908
| | - Joseph A. Lewnard
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720
| | - Estomih R. Mduma
- Haydom Global Health Research Center, Haydom Lutheran Hospital, Haydom, Tanzania
| | - Sanjaya Shrestha
- Walter Reed/AFRIMS Research Unit, Nepal, Kathmandu, 44600, Nepal
| | | | - Pascal O. Bessong
- University of Venda, Thohoyandou, 0950, South Africa
- Center for Global Health Equity, University of Virginia, Charlottesville, VA 22908
| | | | - Margaret Kosek
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA 22908
- Asociación Benéfica PRISMA, Iquitos, 15088, Peru
| | | | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, 1212, Bangladesh
| | - Jie Liu
- School of Public Health, Qingdao University, Qingdao, Shandong, 266071, China
| | - Eric R. Houpt
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA 22908
| | - James A. Platts-Mills
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA 22908
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17
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Antibiotics Drive Expansion of Rare Pathogens in a Chronic Infection Microbiome Model. mSphere 2022; 7:e0031822. [PMID: 35972133 PMCID: PMC9599657 DOI: 10.1128/msphere.00318-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chronic (long-lasting) infections are globally a major and rising cause of morbidity and mortality. Unlike typical acute infections, chronic infections are ecologically diverse, characterized by the presence of a polymicrobial mix of opportunistic pathogens and human-associated commensals. To address the challenge of chronic infection microbiomes, we focus on a particularly well-characterized disease, cystic fibrosis (CF), where polymicrobial lung infections persist for decades despite frequent exposure to antibiotics. Epidemiological analyses point to conflicting results on the benefits of antibiotic treatment yet are confounded by the dependency of antibiotic exposures on prior pathogen presence, limiting their ability to draw causal inferences on the relationships between antibiotic exposure and pathogen dynamics. To address this limitation, we develop a synthetic infection microbiome model representing CF metacommunity diversity and benchmark on clinical data. We show that in the absence of antibiotics, replicate microbiome structures in a synthetic sputum medium are highly repeatable and dominated by oral commensals. In contrast, challenge with physiologically relevant antibiotic doses leads to substantial community perturbation characterized by multiple alternate pathogen-dominant states and enrichment of drug-resistant species. These results provide evidence that antibiotics can drive the expansion (via competitive release) of previously rare opportunistic pathogens and offer a path toward microbiome-informed conditional treatment strategies. IMPORTANCE We develop and clinically benchmark an experimental model of the cystic fibrosis (CF) lung infection microbiome to investigate the impacts of antibiotic exposures on chronic, polymicrobial infections. We show that a single experimental model defined by metacommunity data can partially recapitulate the diversity of individual microbiome states observed across a population of people with CF. In the absence of antibiotics, we see highly repeatable community structures, dominated by oral microbes. Under clinically relevant antibiotic exposures, we see diverse and frequently pathogen-dominated communities, and a nonevolutionary enrichment of antimicrobial resistance on the community scale, mediated by competitive release. The results highlight the potential importance of nonevolutionary (community-ecological) processes in driving the growing global crisis of increasing antibiotic resistance.
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18
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Jamrozik E, Heriot GS. Ethics and antibiotic resistance. Br Med Bull 2022; 141:4-14. [PMID: 35136968 PMCID: PMC8935610 DOI: 10.1093/bmb/ldab030] [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: 07/04/2021] [Revised: 11/28/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022]
Abstract
INTRODUCTION OR BACKGROUND Antibiotic resistance raises ethical issues due to the severe and inequitably distributed consequences caused by individual actions and policies. SOURCES OF DATA Synthesis of ethical, scientific and clinical literature. AREAS OF AGREEMENT Ethical analyses have focused on the moral responsibilities of patients to complete antibiotic courses, resistance as a tragedy of the commons and attempts to limit use through antibiotic stewardship. AREAS OF CONTROVERSY Each of these analyses has significant limitations and can result in self-defeating or overly narrow implications for policy. GROWING POINTS More complex analyses focus on ethical implications of ubiquitous asymptomatic carriage of resistant bacteria, non-linear outcomes within and between patients over time and global variation in resistant disease burdens. AREAS TIMELY FOR DEVELOPING RESEARCH Neglected topics include the harms of antibiotic use, including off-target effects on the human microbiome, and the lack of evidence guiding most antibiotic prescription decisions.
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Affiliation(s)
- Euzebiusz Jamrozik
- The Ethox Centre and Wellcome Centre for Ethics and Humanities, Nuffield Department of Population Health, University of Oxford. Old Road Campus, Oxford OX3 7LF, UK.,Monash Bioethics Centre, Monash University, Wellington Rd, Clayton, 3800, Victoria, Australia.,Department of Medicine, Royal Melbourne Hospital, University of Melbourne, 300 Grattan St, Parkville, 3050, Victoria, Australia
| | - George S Heriot
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, 300 Grattan St, Parkville, 3050, Victoria, Australia
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19
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Staphylococcus massiliensis isolated from human blood cultures, Germany, 2017-2020. Eur J Clin Microbiol Infect Dis 2022; 41:663-669. [PMID: 35079932 PMCID: PMC8789367 DOI: 10.1007/s10096-022-04409-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/18/2022] [Indexed: 11/06/2022]
Abstract
Clinical and laboratory data on newly described staphylococcal species is rare, which hampers decision-making when such pathogens are detected in clinical specimens. Here, we describe Staphylococcus massiliensis detected in three patients at a university hospital in southwest Germany. We report the discrepancy of microbiological findings between matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, 16S-rRNA polymerase chain reaction, and whole-genome sequencing for all three isolates. Our findings highlight the diagnostic pitfalls pertinent to novel and non-model organisms in daily microbiological practice, in whom the correct identification is dependent on database accuracy.
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20
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Kuosmanen T, Cairns J, Noble R, Beerenwinkel N, Mononen T, Mustonen V. Drug-induced resistance evolution necessitates less aggressive treatment. PLoS Comput Biol 2021; 17:e1009418. [PMID: 34555024 PMCID: PMC8491903 DOI: 10.1371/journal.pcbi.1009418] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 10/05/2021] [Accepted: 09/03/2021] [Indexed: 12/24/2022] Open
Abstract
Increasing body of experimental evidence suggests that anticancer and antimicrobial therapies may themselves promote the acquisition of drug resistance by increasing mutability. The successful control of evolving populations requires that such biological costs of control are identified, quantified and included to the evolutionarily informed treatment protocol. Here we identify, characterise and exploit a trade-off between decreasing the target population size and generating a surplus of treatment-induced rescue mutations. We show that the probability of cure is maximized at an intermediate dosage, below the drug concentration yielding maximal population decay, suggesting that treatment outcomes may in some cases be substantially improved by less aggressive treatment strategies. We also provide a general analytical relationship that implicitly links growth rate, pharmacodynamics and dose-dependent mutation rate to an optimal control law. Our results highlight the important, but often neglected, role of fundamental eco-evolutionary costs of control. These costs can often lead to situations, where decreasing the cumulative drug dosage may be preferable even when the objective of the treatment is elimination, and not containment. Taken together, our results thus add to the ongoing criticism of the standard practice of administering aggressive, high-dose therapies and motivate further experimental and clinical investigation of the mutagenicity and other hidden collateral costs of therapies.
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Affiliation(s)
- Teemu Kuosmanen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Johannes Cairns
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Robert Noble
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Present address: Department of Mathematics, City, University of London, London, United Kingdom
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Tommi Mononen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
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21
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Mc Gann P, Geringer MR, Hall LR, Lebreton F, Markelz E, Kwak YI, Johnson S, Ong AC, Powell A, Tekle T, Bergman Y, Simner PJ, Bennett JW, Cybulski RJ, White BK. Pan-drug resistant Providencia rettgeri contributing to a fatal case of COVID-19. J Med Microbiol 2021; 70. [PMID: 34448689 PMCID: PMC8513626 DOI: 10.1099/jmm.0.001406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Following prolonged hospitalization that included broad-spectrum antibiotic exposure, a strain of Providencia rettgeri was cultured from the blood of a patient undergoing extracorporeal membrane oxygenation treatment for hypoxic respiratory failure due to COVID-19. The strain was resistant to all antimicrobials tested including the novel siderophore cephalosporin, cefiderocol. Whole genome sequencing detected ten antimicrobial resistance genes, including the metallo-β-lactamase bla NDM-1, the extended-spectrum β-lactamase bla PER-1, and the rare 16S methyltransferase rmtB2.
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Affiliation(s)
- Patrick Mc Gann
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Matthew R Geringer
- Infectious Disease Service, Brooke Army Medical Center, San Antonio, Texas, USA
| | - Lindsey R Hall
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Elizabeth Markelz
- Infectious Disease Service, Brooke Army Medical Center, San Antonio, Texas, USA
| | - Yoon I Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Sheila Johnson
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ana C Ong
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Aubrey Powell
- Department of Pathology and Area Laboratory Services, Brooke Army Medical Center, San Antonio, Texas, USA
| | - Tsigereda Tekle
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yehudit Bergman
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jason W Bennett
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Robert J Cybulski
- Department of Pathology and Area Laboratory Services, Brooke Army Medical Center, San Antonio, Texas, USA
| | - Brian K White
- Infectious Disease Service, Brooke Army Medical Center, San Antonio, Texas, USA
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22
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Palace SG, Fryling KE, Li Y, Wentworth AJ, Traverso G, Grad YH. Identification of bile acid and fatty acid species as candidate rapidly bactericidal agents for topical treatment of gonorrhoea. J Antimicrob Chemother 2021; 76:2569-2577. [PMID: 34245280 DOI: 10.1093/jac/dkab217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Novel therapeutic strategies are urgently needed for Neisseria gonorrhoeae, given its increasing antimicrobial resistance. Treatment of oropharyngeal N. gonorrhoeae infections has proven particularly challenging, with most reported treatment failures of the first-line drug ceftriaxone occurring at this site and lower cure rates in recent trials of new antibiotics reported for oropharyngeal infections compared with other sites of infection. However, the accessibility of the oropharynx to topical therapeutics provides an opportunity for intervention. Local delivery of a therapeutic at a high concentration would enable the use of non-traditional antimicrobial candidates, including biological molecules that exploit underlying chemical sensitivities of N. gonorrhoeae but lack the potency or pharmacokinetic profiles required for effective systemic administration. METHODS Two classes of molecules that are thought to limit gonococcal viability in vivo, bile acids and short- and medium-chain fatty acids, were examined for rapid bactericidal activity. RESULTS The bile acids deoxycholic acid (DCA) and chenodeoxycholic acid (CDCA), but not other bile acid species, exerted extremely rapid bactericidal properties against N. gonorrhoeae, reducing viability more than 100 000-fold after 1 min. The short-chain fatty acids formic acid and hexanoic acid shared this rapid bactericidal activity. All four molecules are effective against a phylogenetically diverse panel of N. gonorrhoeae strains, including clinical isolates with upregulated efflux pumps and resistance alleles to the most widely used classes of existing antimicrobials. DCA and CDCA are both approved therapeutics for non-infectious indications and are well-tolerated by cultured epithelial cells. CONCLUSIONS DCA and CDCA are attractive candidates for further development as anti-gonococcal agents.
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Affiliation(s)
- Samantha G Palace
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Kyra E Fryling
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Ying Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam J Wentworth
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Giovanni Traverso
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Division of Gastroenterology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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23
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Demers EG, Stajich JE, Ashare A, Occhipinti P, Hogan DA. Balancing Positive and Negative Selection: In Vivo Evolution of Candida lusitaniae MRR1. mBio 2021; 12:e03328-20. [PMID: 33785623 PMCID: PMC8092287 DOI: 10.1128/mbio.03328-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
The evolution of pathogens in response to selective pressures present during chronic infections can influence their persistence and virulence and the outcomes of antimicrobial therapy. Because subpopulations within an infection can be spatially separated and the host environment can fluctuate, an appreciation of the pathways under selection may be most easily revealed through the analysis of numerous isolates from single infections. Here, we continued our analysis of a set of clonally derived Clavispora (Candida) lusitaniae isolates from a single chronic lung infection with a striking enrichment in the number of alleles of MRR1 Genetic and genomic analyses found evidence for repeated acquisition of gain-of-function mutations that conferred constitutive Mrr1 activity. In the same population, there were multiple alleles with both gain-of-function mutations and secondary suppressor mutations that either attenuated or abolished the constitutive activity, suggesting the presence of counteracting selective pressures. Our studies demonstrated trade-offs between high Mrr1 activity, which confers resistance to the antifungal fluconazole, host factors, and bacterial products through its regulation of MDR1, and resistance to hydrogen peroxide, a reactive oxygen species produced in the neutrophilic environment associated with this infection. This inverse correlation between high Mrr1 activity and hydrogen peroxide resistance was observed in multiple Candida species and in serially collected populations from this individual over 3 years. These data lead us to propose that dynamic or variable selective pressures can be reflected in population genomics and that these dynamics can complicate the drug resistance profile of the population.IMPORTANCE Understanding microbial evolution within patients is critical for managing chronic infections and understanding host-pathogen interactions. Here, our analysis of multiple MRR1 alleles in isolates from a single Clavispora (Candida) lusitaniae infection revealed the selection for both high and low Mrr1 activity. Our studies reveal trade-offs between high Mrr1 activity, which confers resistance to the commonly used antifungal fluconazole, host antimicrobial peptides, and bacterial products, and resistance to hydrogen peroxide. This work suggests that spatial or temporal differences within chronic infections can support a large amount of dynamic and parallel evolution and that Mrr1 activity is under both positive and negative selective pressure to balance different traits that are important for microbial survival.
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Affiliation(s)
- Elora G Demers
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Alix Ashare
- Dartmouth-Hitchcock Medical Center, Section of Pulmonary and Critical Care Medicine, Lebanon, New Hampshire, USA
| | - Patricia Occhipinti
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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24
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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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25
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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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26
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Cairns J, Jokela R, Becks L, Mustonen V, Hiltunen T. Repeatable ecological dynamics govern the response of experimental communities to antibiotic pulse perturbation. Nat Ecol Evol 2020; 4:1385-1394. [PMID: 32778754 DOI: 10.1038/s41559-020-1272-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/03/2020] [Indexed: 12/31/2022]
Abstract
In an era of pervasive anthropogenic ecological disturbances, there is a pressing need to understand the factors that constitute community response and resilience. A detailed understanding of disturbance response needs to go beyond associations and incorporate features of disturbances, species traits, rapid evolution and dispersal. Multispecies microbial communities that experience antibiotic perturbation represent a key system with important medical dimensions. However, previous microbiome studies on this theme have relied on high-throughput sequencing data from uncultured species without the ability to explicitly account for the role of species traits and immigration. Here, we serially passage a 34-species defined bacterial community through different levels of pulse antibiotic disturbance, manipulating the presence or absence of species immigration. To understand the ecological community response measured using amplicon sequencing, we combine initial trait data measured for each species separately and metagenome sequencing data revealing adaptive mutations during the experiment. We found that the ecological community response was highly repeatable within the experimental treatments, which could be attributed in part to key species traits (antibiotic susceptibility and growth rate). Increasing antibiotic levels were also coupled with an increasing probability of species extinction, making species immigration critical for community resilience. Moreover, we detected signals of antibiotic-resistance evolution occurring within species at the same time scale, leaving evolutionary changes in communities despite recovery at the species compositional level. Together, these observations reveal a disturbance response that presents as classic species sorting, but is nevertheless accompanied by rapid within-species evolution.
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Affiliation(s)
- Johannes Cairns
- Wellcome Sanger Institute, Cambridge, UK. .,Organismal and Evolutionary Biology Research Programme (OEB), Department of Computer Science, University of Helsinki, Helsinki, Finland. .,Department of Microbiology, University of Helsinki, Helsinki, Finland.
| | - Roosa Jokela
- Department of Microbiology, University of Helsinki, Helsinki, Finland.,Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Lutz Becks
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Aquatic Ecology and Evolution, Limnological Institute University Konstanz, Konstanz, Germany
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme (OEB), Department of Computer Science, University of Helsinki, Helsinki, Finland.,Helsinki Institute for Information Technology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Teppo Hiltunen
- Department of Microbiology, University of Helsinki, Helsinki, Finland. .,Department of Biology, University of Turku, Turku, Finland.
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27
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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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28
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Krieger MS, Denison CE, Anderson TL, Nowak MA, Hill AL. Population structure across scales facilitates coexistence and spatial heterogeneity of antibiotic-resistant infections. PLoS Comput Biol 2020; 16:e1008010. [PMID: 32628660 PMCID: PMC7365476 DOI: 10.1371/journal.pcbi.1008010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/16/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022] Open
Abstract
Antibiotic-resistant infections are a growing threat to human health, but basic features of the eco-evolutionary dynamics remain unexplained. Most prominently, there is no clear mechanism for the long-term coexistence of both drug-sensitive and resistant strains at intermediate levels, a ubiquitous pattern seen in surveillance data. Here we show that accounting for structured or spatially-heterogeneous host populations and variability in antibiotic consumption can lead to persistent coexistence over a wide range of treatment coverages, drug efficacies, costs of resistance, and mixing patterns. Moreover, this mechanism can explain other puzzling spatiotemporal features of drug-resistance epidemiology that have received less attention, such as large differences in the prevalence of resistance between geographical regions with similar antibiotic consumption or that neighbor one another. We find that the same amount of antibiotic use can lead to very different levels of resistance depending on how treatment is distributed in a transmission network. We also identify parameter regimes in which population structure alone cannot support coexistence, suggesting the need for other mechanisms to explain the epidemiology of antibiotic resistance. Our analysis identifies key features of host population structure that can be used to assess resistance risk and highlights the need to include spatial or demographic heterogeneity in models to guide resistance management.
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Affiliation(s)
- Madison S. Krieger
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Carson E. Denison
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Thayer L. Anderson
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Martin A. Nowak
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Alison L. Hill
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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29
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Simonson AW, Aronson MR, Medina SH. Supramolecular Peptide Assemblies as Antimicrobial Scaffolds. Molecules 2020; 25:E2751. [PMID: 32545885 PMCID: PMC7355828 DOI: 10.3390/molecules25122751] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/11/2020] [Accepted: 06/11/2020] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial discovery in the age of antibiotic resistance has demanded the prioritization of non-conventional therapies that act on new targets or employ novel mechanisms. Among these, supramolecular antimicrobial peptide assemblies have emerged as attractive therapeutic platforms, operating as both the bactericidal agent and delivery vector for combinatorial antibiotics. Leveraging their programmable inter- and intra-molecular interactions, peptides can be engineered to form higher ordered monolithic or co-assembled structures, including nano-fibers, -nets, and -tubes, where their unique bifunctionalities often emerge from the supramolecular state. Further advancements have included the formation of macroscopic hydrogels that act as bioresponsive, bactericidal materials. This systematic review covers recent advances in the development of supramolecular antimicrobial peptide technologies and discusses their potential impact on future drug discovery efforts.
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Affiliation(s)
- Andrew W. Simonson
- Department of Biomedical Engineering, The Pennsylvania State University, Suite 122, CBE Building, University Park, PA 16802-4400, USA; (A.W.S.); (M.R.A.)
| | - Matthew R. Aronson
- Department of Biomedical Engineering, The Pennsylvania State University, Suite 122, CBE Building, University Park, PA 16802-4400, USA; (A.W.S.); (M.R.A.)
| | - Scott H. Medina
- Department of Biomedical Engineering, The Pennsylvania State University, Suite 122, CBE Building, University Park, PA 16802-4400, USA; (A.W.S.); (M.R.A.)
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802-4400, USA
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30
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Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects. Microorganisms 2019; 7:microorganisms7080251. [PMID: 31405113 PMCID: PMC6722543 DOI: 10.3390/microorganisms7080251] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 07/31/2019] [Accepted: 08/07/2019] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli may innocuously colonize the intestine of healthy subjects or may instigate infections in the gut or in other districts. This study investigated intestinal E. coli isolated from 20 healthy adults. Fifty-one strains were genotyped by molecular fingerprinting and analyzed for genetic and phenotypic traits, encompassing the profile of antibiotic resistance, biofilm production, the presence of surface structures (such as curli and cellulose), and their performance as recipients in conjugation experiments. A phylogroup classification and analysis of 34 virulence determinants, together with genes associated to the pks island (polyketide-peptide genotoxin colibactin) and conjugative elements, was performed. Most of the strains belonged to the phylogroups B1 and B2. The different phylogroups were separated in a principal coordinate space, considering both genetic and functional features, but not considering pulsed-field gel electrophoresis. Within the B2 and F strains, 12 shared the pattern of virulence genes with potential uropathogens. Forty-nine strains were sensitive to all the tested antibiotics. Strains similar to the potential pathogens innocuously inhabited the gut of healthy subjects. However, they may potentially act as etiologic agents of extra-intestinal infections and are susceptible to a wide range of antibiotics. Nevertheless, there is still the possibility to control infections with antibiotic therapy.
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