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Noyes NR, Slizovskiy IB, Singer RS. Beyond Antimicrobial Use: A Framework for Prioritizing Antimicrobial Resistance Interventions. Annu Rev Anim Biosci 2021; 9:313-332. [PMID: 33592160 DOI: 10.1146/annurev-animal-072020-080638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antimicrobial resistance (AMR) is a threat to animal and human health. Antimicrobial use has been identified as a major driver of AMR, and reductions in use are a focal point of interventions to reduce resistance. Accordingly, stakeholders in human health and livestock production have implemented antimicrobial stewardship programs aimed at reducing use. Thus far, these efforts have yielded variable impacts on AMR. Furthermore, scientific advances are prompting an expansion and more nuanced appreciation of the many nonantibiotic factors that drive AMR, as well as how these factors vary across systems, geographies, and contexts. Given these trends, we propose a framework to prioritize AMR interventions. We use this framework to evaluate the impact of interventions that focus on antimicrobial use. We conclude by suggesting that priorities be expanded to include greater consideration of host-microbial interactions that dictate AMR, as well as anthropogenic and environmental systems that promote dissemination of AMR.
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Affiliation(s)
- Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota 55108, USA; ,
| | - Ilya B Slizovskiy
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota 55108, USA; ,
| | - Randall S Singer
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota 55108, USA;
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Mitochondria and Antibiotics: For Good or for Evil? Biomolecules 2021; 11:biom11071050. [PMID: 34356674 PMCID: PMC8301944 DOI: 10.3390/biom11071050] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 01/16/2023] Open
Abstract
The discovery and application of antibiotics in the common clinical practice has undeniably been one of the major medical advances in our times. Their use meant a drastic drop in infectious diseases-related mortality and contributed to prolonging human life expectancy worldwide. Nevertheless, antibiotics are considered by many a double-edged sword. Their extensive use in the past few years has given rise to a global problem: antibiotic resistance. This factor and the increasing evidence that a wide range of antibiotics can damage mammalian mitochondria, have driven a significant sector of the medical and scientific communities to advise against the use of antibiotics for purposes other to treating severe infections. Notwithstanding, a notorious number of recent studies support the use of these drugs to treat very diverse conditions, ranging from cancer to neurodegenerative or mitochondrial diseases. In this context, there is great controversy on whether the risks associated to antibiotics outweigh their promising beneficial features. The aim of this review is to provide insight in the topic, purpose for which the most relevant findings regarding antibiotic therapies have been discussed.
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Nuzzo A, Van Horn S, Traini C, Perry CR, Dumont EF, Scangarella-Oman NE, Gardiner DF, Brown JR. Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944). BMC Microbiol 2021; 21:181. [PMID: 34130619 PMCID: PMC8207760 DOI: 10.1186/s12866-021-02245-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 06/02/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND With increasing concerns about the impact of frequent antibiotic usage on the human microbiome, it is important to characterize the potential for such effects in early antibiotic drug development clinical trials. In a randomised Phase 2a clinical trial study that evaluated the pharmacokinetics of repeated oral doses of gepotidacin, a first-in-chemical-class triazaacenaphthylene antibiotic with a distinct mechanism of action, in adult females with uncomplicated urinary tract infections for gepotidacin (GSK2140944) we evaluated the potential changes in microbiome composition across multiple time points and body-sites ( ClinicalTrials.gov : NCT03568942). RESULTS Samples of gastrointestinal tract (GIT), pharyngeal cavity and vaginal microbiota were collected with consent from 22 patients at three time points relative to the gepotidacin dosing regimen; Day 1 (pre-dose), Day 5 (end of dosing) and Follow-up (Day 28 ± 3 days). Microbiota composition was determined by DNA sequencing of 16S rRNA gene variable region 4 amplicons. By Day 5, significant changes were observed in the microbiome diversity relative to pre-dose across the tested body-sites. However, by the Follow-up visit, microbiome diversity changes were reverted to compositions comparable to Day 1. The greatest range of microbiome changes by body-site were GIT followed by the pharyngeal cavity then vagina. In Follow-up visit samples we found no statistically significant occurrences of pathogenic taxa. CONCLUSION Our findings suggest that gepotidacin alteration of the human microbiome after 5 days of dosing is temporary and rebound to pre-dosing states is evident within the first month post-treatment. We recommend that future antibiotic drug trials include similar exploratory investigations into the duration and context of microbiome modification and recovery. TRIAL REGISTRATION NCT03568942 . Registered 26 June 2018.
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Affiliation(s)
- Andrea Nuzzo
- Human Genetics, GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY UK
| | | | | | | | | | | | | | - James R. Brown
- Human Genetics, GlaxoSmithKline R&D, Collegeville, PA USA
- Present Address: Kaleido Biosciences, 65 Hayden Avenue, Lexington, MA 02421 USA
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Dixit K, Chaudhari D, Dhotre D, Shouche Y, Saroj S. Restoration of dysbiotic human gut microbiome for homeostasis. Life Sci 2021; 278:119622. [PMID: 34015282 DOI: 10.1016/j.lfs.2021.119622] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
The human microbiome is a complex and dynamic ecosystem, and the imbalance of its microbial community structure from the normal state is termed dysbiosis. The dysbiotic gut microbiome has been proved to be related to several pathological conditions like Inflammatory Bowel Disease (IBD), Irritable Bowel Syndrome (IBS), Colorectal Cancer (CRC), etc., and several other extra-intestinal conditions like Type 1 & 2 diabetes, obesity, etc. The complex gut microbial ecosystem starts to build before the birth of an individual. It is known to get affected by several factors such as birth mode, individual lifestyle, dietary practices, medications, and antibiotics. A dysbiotic microbiome can potentially hamper host homeostasis due to its role in immune modulation, metabolism, nutrient synthesis, etc. Restoration of the dysbiotic gut microbiome has emerged as a promising aid and a better therapeutic approach. Several approaches have been investigated to achieve this goal, including prebiotics and probiotics, Fecal Microbiota Transplantation (FMT), extracellular vesicles, immune modulation, microbial metabolites, dietary interventions, and phages. This review discusses the various factors that influence the human microbiome with respect to their cause-effect relationship and the effect of gut microbiome compositional changes on the brain through the gut-brain axis. We also discuss the practices used globally for gut microbiome restoration purposes, along with their effectiveness.
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Affiliation(s)
- Kunal Dixit
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India
| | - Diptaraj Chaudhari
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune, India
| | - Dhiraj Dhotre
- Innovative Technology Group, Reliance Life Sciences Pvt Ltd., Navi-Mumbai, India
| | - Yogesh Shouche
- National Center for Microbial Resource (NCMR), National Center for Cell Science (NCCS), Pune, India
| | - Sunil Saroj
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, India.
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A guide to human microbiome research: study design, sample collection, and bioinformatics analysis. Chin Med J (Engl) 2021; 133:1844-1855. [PMID: 32604176 PMCID: PMC7469990 DOI: 10.1097/cm9.0000000000000871] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The purpose of this review is to provide medical researchers, especially those without a bioinformatics background, with an easy-to-understand summary of the concepts and technologies used in microbiome research. First, we define primary concepts such as microbiota, microbiome, and metagenome. Then, we discuss study design schemes, the methods of sample size calculation, and the methods for improving the reliability of research. We emphasize the importance of negative and positive controls in this section. Next, we discuss statistical analysis methods used in microbiome research, focusing on problems with multiple comparisons and ways to compare β-diversity between groups. Finally, we provide step-by-step pipelines for bioinformatics analysis. In summary, the meticulous study design is a key step to obtaining meaningful results, and appropriate statistical methods are important for accurate interpretation of microbiome data. The step-by-step pipelines provide researchers with insights into newly developed bioinformatics analysis methods.
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Affiliation(s)
- Sharon V. Tsay
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Adam L. Hersh
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City
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Werner M, Unterer S. [Use of antimicrobials in acute canine diarrhea - overview of potential risks, indications and alternatives]. TIERAERZTLICHE PRAXIS AUSGABE KLEINTIERE HEIMTIERE 2021; 49:110-120. [PMID: 33902119 DOI: 10.1055/a-1395-2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In Germany, antibiotics are frequently used in dogs with gastrointestinal disorders such as acute diarrhea. In line with global efforts to limit antibiotic use, this literature review aims to provide a guideline for the rational and judicious use of antibiotics in acute canine diarrhea. Antibiotics can lead to gastrointestinal side effects and may exert a negative influence on the intestinal microbiota in addition to increasing the occurrence of resistant bacteria. There is also evidence that chronic immunological diseases may be triggered by the administration of antibiotics. Therefore, these should not be administered in uncomplicated acute diarrhea without signs of sepsis or systemic inflammatory reaction. In addition, enteropathogenic bacteria usually do not play a role in the etiology of acute diarrhea. For select clinical entities such as acute hemorrhagic diarrhea syndrome, antibiotic therapy should only be recommended in cases displaying signs of bacterial translocation with subsequent sepsis. In the case of parvovirosis, on the other hand, the administration of antibiotics is unavoidable due to the immunological incompetence of the dog caused by the accompanying severe neutropenia.
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Affiliation(s)
- Melanie Werner
- Medizinische Kleintierklinik, Zentrum für Klinische Tiermedizin, Ludwig-Maximilians-Universität München
| | - Stefan Unterer
- Medizinische Kleintierklinik, Zentrum für Klinische Tiermedizin, Ludwig-Maximilians-Universität München
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Margolis EB, Hakim H, Dallas RH, Allison KJ, Ferrolino J, Sun Y, Pui CH, Yao J, Chang TC, Hayden RT, Jeha S, Tuomanen EI, Tang L, Rosch JW, Wolf J. Antibiotic prophylaxis and the gastrointestinal resistome in paediatric patients with acute lymphoblastic leukaemia: a cohort study with metagenomic sequencing analysis. THE LANCET. MICROBE 2021; 2:e159-e167. [PMID: 34355208 PMCID: PMC8336918 DOI: 10.1016/s2666-5247(20)30202-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Although antibiotic prophylaxis with levofloxacin can reduce the risk of serious infection in immunocompromised patients, the potential contribution of prophylaxis to antibiotic resistance is a major drawback. We aimed to identify the effects of levofloxacin prophylaxis, given to paediatric patients with acute lymphoblastic leukaemia to prevent infections during induction chemotherapy, on antibiotic resistance in gastrointestinal microbiota after completion of induction and consolidation therapy. METHODS This prospective, single-centre (St Jude Children's Research Hospital, Memphis, TN, USA) cohort study included children (≤18 years) receiving therapy for newly diagnosed acute lymphoblastic leukaemia and who received either primary levofloxacin prophylaxis or no antibacterial prophylaxis (aside from Pneumocystis jirovecii prophylaxis with trimethoprim-sulfamethoxazole) and provided at least two stool samples, including one after completion of induction therapy. We used metagenomic sequencing to identify bacterial genes that confer resistance to fluoroquinolones, trimethoprim-sulfamethoxazole, or other antibiotics, and to identify point mutations in bacterial topoisomerases (gyrA, parC) that confer resistance to fluoroquinolones. We then used generalised linear mixed models to compare the prevalence and relative abundance of antibiotic resistance gene groups after completion of induction and consolidation therapy between participants who had received levofloxacin and those who received no prophylaxis. FINDINGS Between Feb 1, 2012, and April 30, 2016, 118 stool samples (32 baseline, 49 after induction, and 37 after consolidation) were collected from 49 evaluable participants; of these participants, 31 (63%) received levofloxacin prophylaxis during induction therapy and 18 (37%) received no antibacterial prophylaxis. Over the course of induction therapy, there was an overall increase in the relative abundance of trimethoprim-sulfamethoxazole resistance genes (estimated mean fold change 5·9, 95% CI 3·6-9·6; p<0·0001), which was not modified by levofloxacin prophylaxis (p=0·46). By contrast, the prevalence of topoisomerase point mutations increased over the course of induction therapy in levofloxacin recipients (mean prevalence 10·4% [95% CI 3·2-25·4] after induction therapy vs 3·7% [0·2-22·5] at baseline) but not other participants (0% vs 0%; p<0·0001). There was no significant difference between prophylaxis groups with respect to changes in aminoglycoside, β-lactam, vancomycin, or multidrug resistance genes after completion of induction or consolidation therapy. INTERPRETATION Analysing the gastrointestinal resistome can provide insights into the effects of antibiotics on the risk of antibiotic-resistant infections. In this study, antibiotic prophylaxis with trimethoprim-sulfamethoxazole or levofloxacin during induction therapy for acute lymphoblastic leukaemia appeared to increase the short-term and medium-term risk of colonisation with bacteria resistant to these antibiotics, but not to other drugs. More research is needed to determine the longer-term effects of antibacterial prophylaxis on colonisation with antibiotic-resistant bacteria. FUNDING Children's Infection Defense Center at St Jude Children's Research Hospital, American Lebanese Syrian Associated Charities, and National Institutes of Health.
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Affiliation(s)
- Elisa B Margolis
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hana Hakim
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ronald H Dallas
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kim J Allison
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jose Ferrolino
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yilun Sun
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jiangwei Yao
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ti-Cheng Chang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Randall T Hayden
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sima Jeha
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Elaine I Tuomanen
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Li Tang
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Joshua Wolf
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
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Stercz B, Farkas FB, Tóth Á, Gajdács M, Domokos J, Horváth V, Ostorházi E, Makra N, Kocsis B, Juhász J, Ligeti B, Pongor S, Szabó D. The influence of antibiotics on transitory resistome during gut colonization with CTX-M-15 and OXA-162 producing Klebsiella pneumoniae ST15. Sci Rep 2021; 11:6335. [PMID: 33737655 PMCID: PMC7973416 DOI: 10.1038/s41598-021-85766-6] [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: 11/23/2020] [Accepted: 02/16/2021] [Indexed: 12/14/2022] Open
Abstract
Great efforts have been made to limit the transmission of carbapenemase-producing Enterobacteriaceae (CPE), however, the intestinal reservoir of these strains and its modulation by various antibiotics remain largely unexplored. Our aim was to assess the effects of antibiotic administration (ampicillin, ceftazidime, ciprofloxacin) on the establishment and elimination of intestinal colonization with a CTX-M-15 ESBL and OXA-162 carbapenemase producing Klebsiella pneumoniae ST15 (KP5825) in a murine (C57BL/6 male mice) model. Whole genome sequencing of KP5825 strain was performed on an Illumina MiSeq platform. Conjugation assays were carried out by broth mating method. In colonization experiments, 5 × 106 CFU of KP5825 was administered to the animals by orogastric gavage, and antibiotics were administered in their drinking water for two weeks and were changed every day. The gut colonization rates with KP5825 were assessed by cultivation and qPCR. In each of the stool samples, the gene copy number of blaOXA-162 and blaCTX-M-15 were determined by qPCR. Antibiotic concentrations in the stool were determined by high pressure liquid chromatography and a bioanalytical method. The KP5825 contained four different plasmid replicon types, namely IncFII(K), IncL, IncFIB and ColpVC. IncL (containing the blaOXA-162 resistance gene within a Tn1991.2 genetic element) and IncFII(K) (containing the blaCTX-M-15 resistance gene) plasmids were successfully conjugated. During ampicillin and ceftazidime treatments, colonization rate of KP5825 increased, while, ciprofloxacin treatments in both concentrations (0.1 g/L and 0.5 g/L) led to significantly decreased colonization rates. The gene copy number blaOXA-162 correlated with K. pneumoniae in vivo, while a major elevation was observed in the copy number of blaCTX-M-15 from the first day to the fifteenth day in the 0.5 g/L dose ceftazidime treatment group. Our results demonstrate that commonly used antibiotics may have diverse impacts on the colonization rates of intestinally-carried CPE, in addition to affecting the gene copy number of their resistance genes, thus facilitating their stable persistance and dissemination.
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Affiliation(s)
- Balázs Stercz
- Institute of Medical Microbiology, Semmelweis University, Nagyvárad tér 4., 1089, Budapest, Hungary
| | - Ferenc B Farkas
- Institute of Medical Microbiology, Semmelweis University, Nagyvárad tér 4., 1089, Budapest, Hungary
| | - Ákos Tóth
- Department of Bacteriology, Mycology and Parasitology, National Public Health Centre, Albert Flórián út 2-6., 1097, Budapest, Hungary
| | - Márió Gajdács
- Institute of Medical Microbiology, Semmelweis University, Nagyvárad tér 4., 1089, Budapest, Hungary
- Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, Eötvös utca 6., 6720, Szeged, Hungary
| | - Judit Domokos
- Institute of Medical Microbiology, Semmelweis University, Nagyvárad tér 4., 1089, Budapest, Hungary
| | - Viola Horváth
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4., 1111, Budapest, Hungary
- MTA-BME Computation Driven Chemistry Research Group, Szent Gellért tér 4., 1111, Budapest, Hungary
| | - Eszter Ostorházi
- Institute of Medical Microbiology, Semmelweis University, Nagyvárad tér 4., 1089, Budapest, Hungary
| | - Nóra Makra
- Institute of Medical Microbiology, Semmelweis University, Nagyvárad tér 4., 1089, Budapest, Hungary
| | - Béla Kocsis
- Institute of Medical Microbiology, Semmelweis University, Nagyvárad tér 4., 1089, Budapest, Hungary
| | - János Juhász
- Faculty of Information Technology and Bionics, Péter Pázmány Catholic University, Práter utca 50/A., 1083, Budapest, Hungary
| | - Balázs Ligeti
- Faculty of Information Technology and Bionics, Péter Pázmány Catholic University, Práter utca 50/A., 1083, Budapest, Hungary
| | - Sándor Pongor
- Faculty of Information Technology and Bionics, Péter Pázmány Catholic University, Práter utca 50/A., 1083, Budapest, Hungary
| | - Dóra Szabó
- Institute of Medical Microbiology, Semmelweis University, Nagyvárad tér 4., 1089, Budapest, Hungary.
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Fecal Microbiome and Resistome Profiling of Healthy and Diseased Pakistani Individuals Using Next-Generation Sequencing. Microorganisms 2021; 9:microorganisms9030616. [PMID: 33802711 PMCID: PMC8002588 DOI: 10.3390/microorganisms9030616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
In this paper, we aimed to characterize the fecal microbiome and its resistomes of healthy and diseased subjects infected with multidrug-resistant Escherichia coli using next-generation sequencing (NGS). After initial screening, 26 stools samples belonging to healthy (n = 13) and diseased subjects (n = 13) were selected and subjected to NGS. A total of 23 and 42 antibiotic-resistant genes (ARGs) conferring resistance to 6 and 9 classes of antibiotics were identified in the resistomes of healthy and diseased subjects, respectively. Bacteroidetes were found to be the major phylum in both healthy and diseased subjects; however, Proteobacteria was predominantly present in the diseased subjects only. Microbial dysbiosis and predominance of various ARGs in the resistome of diseased subjects reflect the excessive usage of antibiotics in Pakistan and warrants immediate attention to regulate the use of various antimicrobials.
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Cugini C, Ramasubbu N, Tsiagbe VK, Fine DH. Dysbiosis From a Microbial and Host Perspective Relative to Oral Health and Disease. Front Microbiol 2021; 12:617485. [PMID: 33763040 PMCID: PMC7982844 DOI: 10.3389/fmicb.2021.617485] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/09/2021] [Indexed: 12/14/2022] Open
Abstract
The significance of microbiology and immunology with regard to caries and periodontal disease gained substantial clinical or research consideration in the mid 1960's. This enhanced emphasis related to several simple but elegant experiments illustrating the relevance of bacteria to oral infections. Since that point, the understanding of oral diseases has become increasingly sophisticated and many of the original hypotheses related to disease causality have either been abandoned or amplified. The COVID pandemic has reminded us of the importance of history relative to infectious diseases and in the words of Churchill "those who fail to learn from history are condemned to repeat it." This review is designed to present an overview of broad general directions of research over the last 60 years in oral microbiology and immunology, reviewing significant contributions, indicating emerging foci of interest, and proposing future directions based on technical advances and new understandings. Our goal is to review this rich history (standard microbiology and immunology) and point to potential directions in the future (omics) that can lead to a better understanding of disease. Over the years, research scientists have moved from a position of downplaying the role of bacteria in oral disease to one implicating bacteria as true pathogens that cause disease. More recently it has been proposed that bacteria form the ecological first line of defense against "foreign" invaders and also serve to train the immune system as an acquired host defensive stimulus. While early immunological research was focused on immunological exposure as a modulator of disease, the "hygiene hypothesis," and now the "old friends hypothesis" suggest that the immune response could be trained by bacteria for long-term health. Advanced "omics" technologies are currently being used to address changes that occur in the host and the microbiome in oral disease. The "omics" methodologies have shaped the detection of quantifiable biomarkers to define human physiology and pathologies. In summary, this review will emphasize the role that commensals and pathobionts play in their interaction with the immune status of the host, with a prediction that current "omic" technologies will allow researchers to better understand disease in the future.
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Affiliation(s)
- Carla Cugini
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, United States
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Fassarella M, Blaak EE, Penders J, Nauta A, Smidt H, Zoetendal EG. Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health. Gut 2021; 70:595-605. [PMID: 33051190 DOI: 10.1136/gutjnl-2020-321747] [Citation(s) in RCA: 240] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022]
Abstract
The human gut microbiome is a complex ecosystem, densely colonised by thousands of microbial species. It varies among individuals and depends on host genotype and environmental factors, such as diet and antibiotics. In this review, we focus on stability and resilience as essential ecological characteristics of the gut microbiome and its relevance for human health. Microbial diversity, metabolic flexibility, functional redundancy, microbe-microbe and host-microbe interactions seem to be critical for maintaining resilience. The equilibrium of the gut ecosystem can be disrupted by perturbations, such as antibiotic therapy, causing significant decreases in functional richness and microbial diversity as well as impacting metabolic health. As a consequence, unbalanced states or even unhealthy stable states can develop, potentially leading to or supporting diseases. Accordingly, strategies have been developed to manipulate the gut microbiome in order to prevent or revert unhealthy states caused by perturbations, including faecal microbiota transplantation, supplementation with probiotics or non-digestible carbohydrates, and more extensive dietary modifications. Nevertheless, an increasing number of studies has evidenced interindividual variability in extent and direction of response to diet and perturbations, which has been attributed to the unique characteristics of each individual's microbiome. From a clinical, translational perspective, the ability to improve resilience of the gut microbial ecosystem prior to perturbations, or to restore its equilibrium afterwards, would offer significant benefits. To be effective, this therapeutic approach will likely need a personalised or subgroup-based understanding of individual genetics, diet, gut microbiome and other environmental factors that might be involved.
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Affiliation(s)
- Marina Fassarella
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ellen E Blaak
- Department of Human Biology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - John Penders
- Department of Medical Microbiology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Arjen Nauta
- FrieslandCampina, Amersfoort, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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Kim DW, Cha CJ. Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission. Exp Mol Med 2021; 53:301-309. [PMID: 33642573 PMCID: PMC8080597 DOI: 10.1038/s12276-021-00569-z] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 01/31/2023] Open
Abstract
The concept of the antibiotic resistome was introduced just over a decade ago, and since then, active resistome studies have been conducted. In the present study, we describe the previously established concept of the resistome, which encompasses all types of antibiotic resistance genes (ARGs), and the important findings from each One-Health sector considering this concept, thereby emphasizing the significance of the One-Health approach in understanding ARG transmission. Cutting-edge research methodologies are essential for deciphering the complex resistome structure in the microbiomes of humans, animals, and the environment. Based on the recent achievements of resistome studies in multiple One-Health sectors, future directions for resistome research have been suggested to improve the understanding and control of ARG transmission: (1) ranking the critical ARGs and their hosts; (2) understanding ARG transmission at the interfaces of One-Health sectors; (3) identifying selective pressures affecting the emergence, transmission, and evolution of ARGs; and (4) elucidating the mechanisms that allow an organism to overcome taxonomic barriers in ARG transmission.
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Affiliation(s)
- Dae-Wi Kim
- grid.411545.00000 0004 0470 4320Division of Life Sciences, Jeonbuk National University, Jeonju, 54896 Republic of Korea
| | - Chang-Jun Cha
- grid.254224.70000 0001 0789 9563Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546 Republic of Korea
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Verdier C, Denis S, Gasc C, Boucinha L, Uriot O, Delmas D, Dore J, Le Camus C, Schwintner C, Blanquet-Diot S. An Oral FMT Capsule as Efficient as an Enema for Microbiota Reconstruction Following Disruption by Antibiotics, as Assessed in an In Vitro Human Gut Model. Microorganisms 2021; 9:microorganisms9020358. [PMID: 33670255 PMCID: PMC7918368 DOI: 10.3390/microorganisms9020358] [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] [Received: 01/12/2021] [Revised: 02/02/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Fecal microbiota transplantation (FMT) is an innovative therapy already used in humans to treat Clostridioides difficile infections associated with massive use of antibiotics. Clinical studies are obviously the gold standard to evaluate FMT efficiency but remain limited by regulatory, ethics, and cost constraints. In the present study, an in vitro model of the human colon reproducing medically relevant perturbation of the colonic ecosystem by antibiotherapy was used to compare the efficiency of traditional FMT enema formulations and a new oral capsule in restoring gut microbiota composition and activity. Loss of microbial diversity, shift in bacterial populations, and sharp decrease in fermentation activities induced in vivo by antibiotherapy were efficiently reproduced in the in vitro model, while capturing inter-individual variability of gut microbiome. Oral capsule was as efficient as enema to decrease the number of disturbed days and bacterial load had no effect on enema performance. This study shows the relevance of human colon models as an alternative approach to in vivo assays during preclinical studies for evaluating FMT efficiency. The potential of this in vitro approach could be extended to FMT testing in the management of many digestive or extra-intestinal pathologies where gut microbial dysbiosis has been evidenced such as inflammatory bowel diseases, obesity or cancers.
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Affiliation(s)
- Cécile Verdier
- UMR 454 MEDIS, Université Clermont Auvergne, INRAe, F-63000 Clermont-Ferrand, France; (C.V.); (S.D.); (O.U.)
- MaaT Pharma, F-69007 Lyon, France; (C.G.); (L.B.); (D.D.); (J.D.); (C.L.C.); (C.S.)
| | - Sylvain Denis
- UMR 454 MEDIS, Université Clermont Auvergne, INRAe, F-63000 Clermont-Ferrand, France; (C.V.); (S.D.); (O.U.)
| | - Cyrielle Gasc
- MaaT Pharma, F-69007 Lyon, France; (C.G.); (L.B.); (D.D.); (J.D.); (C.L.C.); (C.S.)
| | - Lilia Boucinha
- MaaT Pharma, F-69007 Lyon, France; (C.G.); (L.B.); (D.D.); (J.D.); (C.L.C.); (C.S.)
| | - Ophélie Uriot
- UMR 454 MEDIS, Université Clermont Auvergne, INRAe, F-63000 Clermont-Ferrand, France; (C.V.); (S.D.); (O.U.)
| | - Dominique Delmas
- MaaT Pharma, F-69007 Lyon, France; (C.G.); (L.B.); (D.D.); (J.D.); (C.L.C.); (C.S.)
| | - Joël Dore
- MaaT Pharma, F-69007 Lyon, France; (C.G.); (L.B.); (D.D.); (J.D.); (C.L.C.); (C.S.)
- MICALIS and MétaGénoPolis, Université Paris Saclay, INRAe, AgroParisTech, F-78350 Jouy-en-Josas, France
| | - Corentin Le Camus
- MaaT Pharma, F-69007 Lyon, France; (C.G.); (L.B.); (D.D.); (J.D.); (C.L.C.); (C.S.)
| | - Carole Schwintner
- MaaT Pharma, F-69007 Lyon, France; (C.G.); (L.B.); (D.D.); (J.D.); (C.L.C.); (C.S.)
| | - Stéphanie Blanquet-Diot
- UMR 454 MEDIS, Université Clermont Auvergne, INRAe, F-63000 Clermont-Ferrand, France; (C.V.); (S.D.); (O.U.)
- Correspondence:
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65
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Chumponsuk T, Gruneck L, Gentekaki E, Jitprasertwong P, Kullawong N, Nakayama J, Popluechai S. The salivary microbiota of Thai adults with metabolic disorders and association with diet. Arch Oral Biol 2021; 122:105036. [PMID: 33421657 DOI: 10.1016/j.archoralbio.2020.105036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/24/2020] [Accepted: 12/26/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVE This study aimed to investigate abundance of specific bacterial taxa in the saliva of 105 Thai adults with different BMI (lean, overweight, and obese) and T2DM subjects using qPCR targeting the 16S rRNA gene of various bacteria taxa. DESIGN We employed qPCR targeting 16S rRNA genes to explore the bacterial profiles and abundances in the saliva of Thai adult subjects with different BMI and T2DM. Multivariate statistical analyses (multiple factor analysis (MFA) and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) were performed to assess the associations of salivary bacteria with diet, blood profile, gender, age, and use of antibiotics. RESULTS We found that abundance profiles of the examined salivary bacteria were similar across the four groups. When diet, blood profile, and gender, age, and use of antibiotics were considered, significant differences were noted between subgroups. A positive correlation was also found between consumption of carbonate soft drinks and Bacteroidetes, Gamma-proteobacteria, Veillonella, Fusobacterium and Fusobacterium nucleatum. CONCLUSIONS This is the first study demonstrating the relative abundance of salivary bacteria in adult Thai subjects with different levels of BMI and T2DM. Regardless of the similar pattern of bacterial profiles across groups, sPLS-DA analysis highlighted the influence of host variables (gender, age, and use of antibiotics) on the abundance of salivary microbiota. Our findings pave the way for further hypothesis testing to gain insight into the association between host factors and salivary microbiome.
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Affiliation(s)
| | - Lucsame Gruneck
- Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai, Thailand
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Muang, Chiang Rai, Thailand; Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai, Thailand
| | - Paiboon Jitprasertwong
- School of Geriatric Oral Health, Institute of Dentistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Niwed Kullawong
- School of Health Science, Mae Fah Luang University, Muang, Chiang Rai, Thailand
| | - Jiro Nakayama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Siam Popluechai
- School of Science, Mae Fah Luang University, Muang, Chiang Rai, Thailand; Gut Microbiome Research Group, Mae Fah Luang University, Muang, Chiang Rai, Thailand.
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66
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Li L, Wang Q, Gao Y, Liu L, Duan Y, Mao D, Luo Y. Colistin and amoxicillin combinatorial exposure alters the human intestinal microbiota and antibiotic resistome in the simulated human intestinal microbiota. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:141415. [PMID: 32846251 DOI: 10.1016/j.scitotenv.2020.141415] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 05/26/2023]
Abstract
Antibiotics treatment could cause the dysbiosis of human intestinal microbiota and antibiotic resistome. Fecal microbiota transplantation (FMT) has been an efficacious treatment to restore the dysbiosis of intestinal microbiota in a variety of intestinal diseases. However, to data, the effect of the combinatorial antibiotic treatment on microbiota, antibiotic resistome and the FMT for restoration affected by combinatorial antibiotic exposure in the human intestinal microbiota remain unclear. In this study, we systematically investigated the effect of the colistin and amoxicillin combinatorial exposure in the simulator of the human intestinal microbial ecosystem (SHIME) and found that this combinatorial exposure significantly altered (p < 0.05) the human intestinal microbiota and antibiotic resistome. The shift of bacterial community and antibiotic resistome could incompletely recovery to baseline by FMT treatment after combinatorial antibiotic exposure. Additionally, the variance of antibiotic resistome was dominantly driven by the bacterial community (41.18%-68.03%) after the combinatorial antibiotic exposure. Overall, this study first to investigate the influence of the colistin and amoxicillin combinatorial exposure on the intestinal microbiota and antibiotic resistome, and assess the FMT recovery in the simulated human intestinal microbiota, which may potentially provide a correct administration of antibiotics and application of FMT in the clinic.
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Affiliation(s)
- Linyun Li
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Qing Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China; College of Energy and Environmental Engineering, Hebei University of Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact (preparatory), Handan 056038, China
| | - Yanyu Gao
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Lei Liu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Yujing Duan
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China.
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67
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Bourke CD, Evans C. Cotrimoxazole Prophylaxis Selects for Antimicrobial Resistance in Human Immunodeficiency Virus-Exposed, Uninfected Infants. Clin Infect Dis 2020; 71:2869-2871. [PMID: 31832637 PMCID: PMC7778347 DOI: 10.1093/cid/ciz1193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 01/01/2023] Open
Affiliation(s)
- Claire D Bourke
- Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Ceri Evans
- Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
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68
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Jaskiw GE, Obrenovich ME, Kundrapu S, Donskey CJ. Changes in the Serum Metabolome of Patients Treated With Broad-Spectrum Antibiotics. Pathog Immun 2020; 5:382-418. [PMID: 33474520 PMCID: PMC7810407 DOI: 10.20411/pai.v5i1.394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/16/2020] [Indexed: 12/14/2022] Open
Abstract
Background: The gut microbiome (GMB) generates numerous small chemicals that can be absorbed by the host and variously biotransformed, incorporated, or excreted. The resulting metabolome can provide information about the state of the GMB, of the host, and of their relationship. Exploiting this information in the service of biomarker development is contingent on knowing the GMB-sensitivity of the individual chemicals comprising the metabolome. In this regard, human studies have lagged far behind animal studies. Accordingly, we tested the hypothesis that serum levels of chemicals unequivocally demonstrated to be GMB-sensitive in rodent models would also be affected in a clinical patient sample treated with broad spectrum antibiotics. Methods: We collected serum samples from 20 hospitalized patients before, during, and after treatment with broad-spectrum antibiotics. We also collected samples from 5 control patients admitted to the hospital but not prescribed antibiotics. We submitted the samples for a non-targeted metabolomic analysis and then focused on chemicals known to be affected both by germ-free status and by antibiotic treatment in the mouse and/or rat. Results: Putative identification was obtained for 499 chemicals in human serum. An aggregate analysis did not show any time x treatment interactions. However, our literature search identified 10 serum chemicals affected both by germ-free status and antibiotic treatment in the mouse or rat. Six of those chemicals were measured in our patient samples and additionally met criteria for inclusion in a focused analysis. Serum levels of 5 chemicals (p-cresol sulfate, phenol sulfate, hippurate, indole propionate, and indoxyl sulfate) declined significantly in our group of antibiotic-treated patients but did not change in our patient control group. Conclusions: Broad-spectrum antibiotic treatment in patients lowered serum levels of selected chemicals previously demonstrated to be GMB-sensitive in rodent models. Interestingly, all those chemicals are known to be uremic solutes that can be derived from aromatic amino acids (L-phenylalanine, L-tyrosine, or L-tryptophan) by anaerobic bacteria, particularly Clostridial species. We conclude that judiciously selected serum chemicals can reliably detect antibiotic-induced suppression of the GMB in man and thus facilitate further metabolome-based biomarker development.
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Affiliation(s)
- George E Jaskiw
- Psychiatry Service, Veterans Affairs Northeast Ohio Healthcare System (VANEOHS), Cleveland, Ohio.,School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Mark E Obrenovich
- Pathology and Laboratory Medicine Service, VANEOHS, Cleveland, Ohio.,Research Service, VANEOHS, Cleveland, Ohio.,Department of Chemistry, Case Western Reserve University, Cleveland, Ohio
| | - Sirisha Kundrapu
- School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Curtis J Donskey
- School of Medicine, Case Western Reserve University, Cleveland, Ohio.,Geriatric Research, Education and Clinical Center, VANEOHS, Cleveland, Ohio
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69
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Kronbichler A, Harrison EM, Wagner J. Nasal microbiome research in ANCA-associated vasculitis: Strengths, limitations, and future directions. Comput Struct Biotechnol J 2020; 19:415-423. [PMID: 33489010 PMCID: PMC7804347 DOI: 10.1016/j.csbj.2020.12.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022] Open
Abstract
The human nasal microbiome is characterized by biodiversity and undergoes changes during the span of life. In granulomatosis with polyangiitis (GPA), the persistent nasal colonization by Staphylococcus aureus (S. aureus) assessed by culture-based detection methods has been associated with increased relapse frequency. Different research groups have characterized the nasal microbiome in patients with GPA and found that patients have a distinct nasal microbiome compared to controls, but the reported results between studies differed. In order to increase comparability, there is a need to standardize patient selection, sample preparation, and analytical methodology; particularly as low biomass samples like those obtained by nasal swabbing are impacted by reagent contamination. Optimization in obtaining a sample and processing with the inclusion of critical controls is needed for consistent comparative studies. Ongoing studies will analyze the nasal microbiome in GPA in a longitudinal way and the results will inform whether or not targeted antimicrobial management in a clinical trial should be pursued or not. This review focuses on the proposed role of S. aureus in GPA, the (healthy) nasal microbiome, findings in the first pilot studies in GPA, and will discuss future strategies.
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Affiliation(s)
- Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
- Department of Medicine, University of Cambridge, CB2 0QQ, United Kingdom
- Corresponding author at: Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria.
| | - Ewan M. Harrison
- Department of Medicine, University of Cambridge, CB2 0QQ, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CD10 1SA, United Kingdom
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, United Kingdom
| | - Josef Wagner
- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, Victoria, Australia
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70
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Xiao Y, Hang Y, Chen Y, Fang X, Cao X, Hu X, Luo H, Zhu H, Zhu W, Zhong Q, Hu L. A Retrospective Analysis of Risk Factors and Patient Outcomes of Bloodstream Infection with Extended-Spectrum β-Lactamase-Producing Escherichia coli in a Chinese Tertiary Hospital. Infect Drug Resist 2020; 13:4289-4296. [PMID: 33262623 PMCID: PMC7699446 DOI: 10.2147/idr.s269989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Objective The present study assessed risk factors and patient outcomes of bloodstream infection (BSI) caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli). Methods A retrospective study was performed to analyze risk factors and patient outcomes of BSI caused by extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) in one Chinese tertiary hospital over a 7.5-year period. The clinical characteristics of patients infected with ESBL-producing and non-ESBL-producing E. coli were compared. Predictors of 30-day mortality in patients with E. coli BSI were also identified in our study. Results The results of drug sensitivity showed that quinolones, aminoglycosides, β-lactam/β-lactamase inhibitor combinations (BLICs) and trimethoprim/sulfamethoxazole exhibited significant differences between the ESBL and non-ESBL groups. Of the 963 patients with E. coli BSI, 57.6% developed ESBL-EC. Multivariate analysis showed that biliary tract infection (BTI) [P<0.001,OR (95% CI):1.798 (1.334–2.425)], urinary tract obstructive disease [P=0.001,OR (95% CI):2.106 (1.366–3.248)], surgery within 3 months [P=0.002,OR (95% CI):1.591 (1.178–2.147)], hospitalization within 3 months [P<0.001,OR (95% CI):2.075 (1.579–2.725)], ICU admission [P=0.011,OR (95% CI):1.684 (1.124–2.522)] and history of cephalosporin use [P=0.006,OR (95% CI):3.097 (1.392–6.891)] were statistically significant. In mortality analysis, aCCI>2 [P=0.016,OR (95% CI): 2.453 (1.179–5.103)], gastrointestinal catheterization [P=0.004, OR (95% CI): 2.525 (1.333–4.782)] were significantly associated with 30-day mortality. According to Kaplan-Meier survival analysis, we found that in SOFA<2 group and SOFA≥2 group, the mortality rate of patients treated with BLICs were lower than that of carbapenems(P<0.05). Conclusion This study showed that BTI, urinary tract obstructive disease, surgery within 3 months, hospitalization within 3 months, ICU admission and cephalosporin exposure were independent risk factors for the emergence of ESBL-EC BSI. Analysis of risk factors for 30-day mortality revealed that the factors independently associated with a higher risk of mortality were aCCI>2, gastrointestinal catheterization. Compared to carbapenems, the BLICs had preferable effect to treat patients with ESBL-EC BSI. Notably, patients with severe illness were inlcined to use carbapenems, which affected the analysis results. Therefore, we suggest that BLICs could be recommended to treat mild patients with ESBL-EC bacteremia.
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Affiliation(s)
- Yanping Xiao
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Yaping Hang
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Yanhui Chen
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xueyao Fang
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xingwei Cao
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xiaoyan Hu
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Hong Luo
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Hongying Zhu
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Wu Zhu
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Qiaoshi Zhong
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Longhua Hu
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
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71
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Duan H, Yu L, Tian F, Zhai Q, Fan L, Chen W. Antibiotic-induced gut dysbiosis and barrier disruption and the potential protective strategies. Crit Rev Food Sci Nutr 2020; 62:1427-1452. [PMID: 33198506 DOI: 10.1080/10408398.2020.1843396] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The oral antibiotic therapies administered widely to people and animals can cause gut dysbiosis and barrier disruption inevitably. Increasing attention has been directed toward antibiotic-induced gut dysbiosis, which involves a loss of diversity, changes in the abundances of certain taxa and consequent effects on their metabolic capacity, and the spread of antibiotic-resistant bacterial strains. Treatment with beta-lactam, glycopeptide, and macrolide antibiotics is associated with the depletion of beneficial commensal bacteria in the genera Bifidobacterium and Lactobacillus. The gut microbiota is a reservoir for antibiotic resistance genes, the prevalence of which increases sharply after antibiotic ingestion. The intestinal barrier, which comprises secretory, physical, and immunological barriers, is also a target of antibiotics. Antibiotic induced changes in the gut microbiota composition could induce weakening of the gut barrier through changes in mucin, cytokine, and antimicrobial peptide production by intestinal epithelial cells. Reports have indicated that dietary interventions involving prebiotics, probiotics, omega-3 fatty acids, and butyrate supplementation, as well as fecal microbiota transplantation, can alleviate antibiotic-induced gut dysbiosis and barrier injuries. This review summarizes the characteristics of antibiotic-associated gut dysbiosis and barrier disruption, as well as the strategies for alleviating this condition. This information is intended to provide a foundation for the exploration of safer, more efficient, and affordable strategies to prevent or relieve antibiotic-induced gut injuries.
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Affiliation(s)
- Hui Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Research Laboratory for Probiotics at, Jiangnan University, Wuxi, Jiangsu, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Research Laboratory for Probiotics at, Jiangnan University, Wuxi, Jiangsu, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Research Laboratory for Probiotics at, Jiangnan University, Wuxi, Jiangsu, China
| | - Liuping Fan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Research Laboratory for Probiotics at, Jiangnan University, Wuxi, Jiangsu, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Research Laboratory for Probiotics at, Jiangnan University, Wuxi, Jiangsu, China
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72
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Zhao R, Yu K, Zhang J, Zhang G, Huang J, Ma L, Deng C, Li X, Li B. Deciphering the mobility and bacterial hosts of antibiotic resistance genes under antibiotic selection pressure by metagenomic assembly and binning approaches. WATER RESEARCH 2020; 186:116318. [PMID: 32871290 DOI: 10.1016/j.watres.2020.116318] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/15/2020] [Accepted: 08/18/2020] [Indexed: 05/21/2023]
Abstract
The presence of antibiotics can exert significant selection pressure on the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). However, co-selection effects for ARGs, the mobility of ARGs and the identification of ARG hosts under high antibiotic selection pressures are poorly understood. Here, metagenomic assembly and binning approaches were used to comprehensively decipher the prevalence of ARGs and their potential mobility and hosts in activated sludge reactors treating antibiotic production wastewater. We found the abundance of different ARG types in antibiotic treatments varied greatly and certain antibiotic pressure promoted the co-selection for the non-corresponding types of ARGs. Antibiotic selection pressures significantly increased the abundance and proportions of ARGs mediated by plasmids (57.9%), which were more prevalent than those encoded in chromosomes (19.2%). The results indicated that plasmids and chromosomes had a tendency to carry different types of ARGs. Moreover, higher co-occurrence frequency of ARGs and MGEs revealed that antibiotics enhanced the mobility potential of ARGs mediated by both plasmids and integrative and conjugative elements. Among the 689 metagenome-assembled genomes (MAGs) with high estimated quality, 119 MAGs assigning to nine bacterial phyla were identified as the ARG hosts and 33 MAGs exhibited possible multi-resistance to antibiotics. Some ARG types tended to be carried by certain bacteria (e.g. bacitracin resistance genes carried by the family Burkholderiaceae) and thus showed a pronounced host-specific pattern. This study enhances the understanding of the mobility and hosts of ARGs and provides important insights into the risk assessment and management of antibiotic resistance.
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Affiliation(s)
- Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Jiayu Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Guijuan Zhang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jin Huang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Liping Ma
- Shanghai Key Laboratory for Urban Ecological Process and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Chunfang Deng
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518055, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
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73
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Schwartz DJ, Langdon AE, Dantas G. Understanding the impact of antibiotic perturbation on the human microbiome. Genome Med 2020; 12:82. [PMID: 32988391 PMCID: PMC7523053 DOI: 10.1186/s13073-020-00782-x] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/11/2020] [Indexed: 02/08/2023] Open
Abstract
The human gut microbiome is a dynamic collection of bacteria, archaea, fungi, and viruses that performs essential functions for immune development, pathogen colonization resistance, and food metabolism. Perturbation of the gut microbiome's ecological balance, commonly by antibiotics, can cause and exacerbate diseases. To predict and successfully rescue such perturbations, first, we must understand the underlying taxonomic and functional dynamics of the microbiome as it changes throughout infancy, childhood, and adulthood. We offer an overview of the healthy gut bacterial architecture over these life stages and comment on vulnerability to short and long courses of antibiotics. Second, the resilience of the microbiome after antibiotic perturbation depends on key characteristics, such as the nature, timing, duration, and spectrum of a course of antibiotics, as well as microbiome modulatory factors such as age, travel, underlying illness, antibiotic resistance pattern, and diet. In this review, we discuss acute and chronic antibiotic perturbations to the microbiome and resistome in the context of microbiome stability and dynamics. We specifically discuss key taxonomic and resistance gene changes that accompany antibiotic treatment of neonates, children, and adults. Restoration of a healthy gut microbial ecosystem after routine antibiotics will require rationally managed exposure to specific antibiotics and microbes. To that end, we review the use of fecal microbiota transplantation and probiotics to direct recolonization of the gut ecosystem. We conclude with our perspectives on how best to assess, predict, and aid recovery of the microbiome after antibiotic perturbation.
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Affiliation(s)
- D. J. Schwartz
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - A. E. Langdon
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - G. Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
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74
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Kreuzer M, Hardt WD. How Food Affects Colonization Resistance Against Enteropathogenic Bacteria. Annu Rev Microbiol 2020; 74:787-813. [DOI: 10.1146/annurev-micro-020420-013457] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Food has a major impact on all aspects of health. Recent data suggest that food composition can also affect susceptibility to infections by enteropathogenic bacteria. Here, we discuss how food may alter the microbiota as well as mucosal defenses and how this can affect infection. Salmonella Typhimurium diarrhea serves as a paradigm, and complementary evidence comes from other pathogens. We discuss the effects of food composition on colonization resistance, host defenses, and the infection process as well as the merits and limitations of mouse models and experimental foods, which are available to decipher the underlying mechanisms.
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Affiliation(s)
- Markus Kreuzer
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
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75
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Lim YY, Lee YS, Ooi DSQ. Engineering the Gut Microbiome for Treatment of Obesity: A Review of Current Understanding and Progress. Biotechnol J 2020; 15:e2000013. [PMID: 32663372 DOI: 10.1002/biot.202000013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 07/07/2020] [Indexed: 12/13/2022]
Abstract
Obesity is a complex, multifactorial disease that is increasing in prevalence despite extensive research and efforts to curb it. Over the last decade, gut microbiome has emerged as an important contributor to the pathogenesis of obesity. Microbiome profile is altered in obese phenotype and the causative role of microbiome in obesity is demonstrated in fecal microbiota transplantation studies. Herein, recent evidences supporting the role of gut microbiome in obesity and the current therapies designed to engineer gut microbiome for treatment of obesity will be reviewed. The microbial enterotypes associated with obesity is outlined, and the gut microbiota-driven metabolism and low-grade inflammation linking gut microbiome and obesity is examined. How the different intrinsic and extrinsic factors such as host genetics, mode of childbirth delivery, diet, lifestyle habits and use of antibiotics influence the composition of the gut microbiome in the development of obesity is evaluated. Also, the efficacy of current microbiome-based therapies in the forms of prebiotics, probiotics and engineered microbes that are used to manipulate gut microbiome in treating obesity is discussed.
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Affiliation(s)
- Yvonne Yijuan Lim
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Division of Paediatric Endocrinology, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, 119228, Singapore
| | - Yung Seng Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Division of Paediatric Endocrinology, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, 119228, Singapore
| | - Delicia Shu Qin Ooi
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Division of Paediatric Endocrinology, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, 119228, Singapore
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76
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Ruiz-Patiño A, Barrón F, Cardona AF, Corrales L, Mas L, Martín C, Zatarain-Barrón ZL, Recondo G, Ricaurte L, Rojas L, Archila P, Rodríguez J, Sotelo C, Viola L, Vargas C, Carranza H, Otero J, Pino LE, Rolfo C, Rosell R, Arrieta O. Antibiotics impair immune checkpoint inhibitor effectiveness in Hispanic patients with non-small cell lung cancer (AB-CLICaP). Thorac Cancer 2020; 11:2552-2560. [PMID: 32705787 PMCID: PMC7471049 DOI: 10.1111/1759-7714.13573] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022] Open
Abstract
Background The intestinal microbiota is an important factor in modulating immune‐mediated tumor cell destruction. Alterations in the microbiome composition have been linked to reduced efficacy of immune checkpoint inhibitor (ICI) therapies. Therefore, antibiotic treatment (ATB), which modifies the diversity of the gut bacteria populations, could lead to a reduced efficacy of ICI treatments. Methods This was a retrospective cohort study. Patients with advanced non‐small cell lung cancer (NSCLC) treated with anti‐programmed cell death ligand‐1 (PD‐L1) alone, or in combination in three different countries in Latin America were included. After identification, patients were placed into three groups: Non‐ATB exposed (no‐ATB), exposed within 30 days of the first dose of ICI (pre‐ICI ATB) and patients receiving ATB concomitantly with ICI (ICI‐ATB). Progression‐free survival (PFS), overall survival (OS) and response rates to treatment with ICI were assessed. Results A total of 140 patients were included, of which 32 patients (23%) received ATB treatment. The most common ATB types were fluoroquinolones and B‐lactams. No differences in survival according to antibiotic type were identified. Median OS in patients not exposed to ATB was 40.6 months (95% CI: 32–67.7), compared with 20.3 months (95% CI: 12.1‐non‐reached [NR]) for patients with pre‐ICI ATB treatment and 24.7 months (95% CI: 13‐NR) for patients treated with ATB concomitantly with ICI. There were no significant differences in terms of PFS, or response rates across all treatment groups. Conclusions Antibiotic treatment was associated with reduced OS in Hispanic patients with NSCLC treated with ICIs.
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Affiliation(s)
- Alejandro Ruiz-Patiño
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (FOX-G), Universidad el Bosque, Bogotá, Colombia
| | - Feliciano Barrón
- Thoracic Oncology Unit, Instituto Nacional de Cancerología, México City, Mexico
| | - Andrés F Cardona
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (FOX-G), Universidad el Bosque, Bogotá, Colombia.,Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia
| | - Luis Corrales
- Medical Oncology Department, Hospital San Juan de Dios, San José, Costa Rica.,Thoracic Oncology Department, Centro de Investigación y Manejo del Cáncer - CIMCA, San José, Costa Rica
| | - Luis Mas
- Oncology Department, Instituto Nacional de Enfermedades Neoplásicas - IneN, Lima, Peru
| | - Claudio Martín
- Medical Oncology Department, Thoracic Oncology Section, Instituto Fleming, Buenos Aires, Argentina
| | | | - Gonzalo Recondo
- Medical Oncology Department, Center for Medical Education and Clinical Research (CEMIC), Buenos Aires, Argentina
| | - Luisa Ricaurte
- Molecular Oncology and Biology Systems Research Group (FOX-G), Universidad el Bosque, Bogotá, Colombia
| | - Leonardo Rojas
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (FOX-G), Universidad el Bosque, Bogotá, Colombia.,Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia.,Clinical Oncology Department, Clínica Colsanitas, Bogotá, Colombia
| | - Pilar Archila
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia
| | - July Rodríguez
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia
| | - Carolina Sotelo
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia
| | - Lucia Viola
- Thoracic Oncology Unit, Fundación Neumológica Colombiana- FNC, Bogotá, Colombia
| | - Carlos Vargas
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (FOX-G), Universidad el Bosque, Bogotá, Colombia.,Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia
| | - Hernán Carranza
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (FOX-G), Universidad el Bosque, Bogotá, Colombia.,Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia
| | - Jorge Otero
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogotá, Colombia.,Molecular Oncology and Biology Systems Research Group (FOX-G), Universidad el Bosque, Bogotá, Colombia
| | - Luis E Pino
- Oncology Department, Institute of Oncology - ICAL, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Christian Rolfo
- Thoracic Oncology Unit, Marlene and Stewart Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland, USA
| | - Rafael Rosell
- Institut d'Investigació en Ciències Germans Trias i Pujol, Badalona, Spain.,Institut Català d'Oncologia, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología, México City, Mexico
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77
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Park IJ, Lee JH, Kye BH, Oh HK, Cho YB, Kim YT, Kim JY, Sung NY, Kang SB, Seo JM, Sim JH, Lee JL, Lee IK. Effects of PrObiotics on the Symptoms and Surgical ouTComes after Anterior REsection of Colon Cancer (POSTCARE): A Randomized, Double-Blind, Placebo-Controlled Trial. J Clin Med 2020; 9:jcm9072181. [PMID: 32664289 PMCID: PMC7408996 DOI: 10.3390/jcm9072181] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/25/2020] [Accepted: 07/02/2020] [Indexed: 01/08/2023] Open
Abstract
We investigated microbiota changes following surgical colon cancer resection and evaluate effects of probiotics on microbiota and surgical recovery. This randomized double-blind trial was performed at four medical centers in South Korea. Of 68 patients expected to undergo anterior sigmoid colon cancer resection, 60 were eligible, of whom 29 and 31 received probiotics and placebo, respectively, for four weeks, starting at one week preoperatively. Third- and/or fourth-week information on anterior resection syndrome (ARS), inflammatory markers, and quality of life was obtained. Stool sample analysis was conducted after randomization and bowel preparation and at three and four postoperative weeks. Bacteria were categorized into Set I (with probiotic effects) and II (colon cancer-associated). The probiotic group’s ARS score showed an improving trend (p = 0.063), particularly for flatus control (p = 0.030). Serum zonulin levels significantly decreased with probiotics. Probiotic ingestion resulted in compositional changes in gut microbiota; greater increases and decreases in Set I and II bacteria, respectively, occurred with probiotics. Compositional increase in Set I bacteria was associated with reduced white blood cells, neutrophils, neutrophil-lymphocyte ratio, and zonulin. Bifidobacterium composition was negatively correlated with zonulin levels in the probiotic group. Probiotics improved postoperative flatus control and modified postoperative changes in microbiota and inflammatory markers.
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Affiliation(s)
- In Ja Park
- Department of Colon and Rectal Surgery, Asan Medical Centre and University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea;
| | - Ju-Hoon Lee
- Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Korea; (J.-H.L.); (Y.-T.K.)
| | - Bong-Hyeon Kye
- Department of Surgery, St. Vincent’s Hospital, College of Medicine, The Catholic University of Korea, 93, Jungbu-daero, Paldal-gu, Suwon-si, Gyeonggi-do 16247, Korea;
| | - Heung-Kwon Oh
- Department of Surgery, Seoul National University Bundang Hospital, 300 Gumi-dong Bundang-gu, Seongnam-si, Gyeonggi-do 13620, Korea; (H.-K.O.); (S.-B.K.)
| | - Yong Beom Cho
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Korea;
| | - You-Tae Kim
- Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University, 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do 17104, Korea; (J.-H.L.); (Y.-T.K.)
| | - Joo Yun Kim
- R&BD Centre, Korea Yakult Co. Ltd., 577, Gangnam-daero, Seocho-gu, Seoul 05505, Korea; (J.Y.K.); (J.-H.S.); (J.-L.L.)
| | - Na Young Sung
- National Cancer Control Institute, National Cancer Centre, 323 Ilsan-ro, Ilsandong-gu, Goyang-si Gyeonggi-do 10408, Korea;
| | - Sung-Bum Kang
- Department of Surgery, Seoul National University Bundang Hospital, 300 Gumi-dong Bundang-gu, Seongnam-si, Gyeonggi-do 13620, Korea; (H.-K.O.); (S.-B.K.)
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Samsung Medical Centre, Sungkyunkwan University School of Medicine, 81 Ilwon-ro, Gangnam-gu, Seoul 06351, Korea;
| | - Jae-Hun Sim
- R&BD Centre, Korea Yakult Co. Ltd., 577, Gangnam-daero, Seocho-gu, Seoul 05505, Korea; (J.Y.K.); (J.-H.S.); (J.-L.L.)
| | - Jung-Lyoul Lee
- R&BD Centre, Korea Yakult Co. Ltd., 577, Gangnam-daero, Seocho-gu, Seoul 05505, Korea; (J.Y.K.); (J.-H.S.); (J.-L.L.)
| | - In Kyu Lee
- Department of Surgery, Division of Colorectal Surgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea
- Correspondence: ; Tel.: +82-2-2258-6104
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78
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Munck C, Sheth RU, Cuaresma E, Weidler J, Stump SL, Zachariah P, Chong DH, Uhlemann AC, Abrams JA, Wang HH, Freedberg DE. The effect of short-course antibiotics on the resistance profile of colonizing gut bacteria in the ICU: a prospective cohort study. Crit Care 2020; 24:404. [PMID: 32646458 PMCID: PMC7350675 DOI: 10.1186/s13054-020-03061-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/04/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The need for early antibiotics in the intensive care unit (ICU) is often balanced against the goal of antibiotic stewardship. Long-course antibiotics increase the burden of antimicrobial resistance within colonizing gut bacteria, but the dynamics of this process are not fully understood. We sought to determine how short-course antibiotics affect the antimicrobial resistance phenotype and genotype of colonizing gut bacteria in the ICU by performing a prospective cohort study with assessments of resistance at ICU admission and exactly 72 h later. METHODS Deep rectal swabs were performed on 48 adults at the time of ICU admission and exactly 72 h later, including patients who did and did not receive antibiotics. To determine resistance phenotype, rectal swabs were cultured for methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE). In addition, Gram-negative bacterial isolates were cultured against relevant antibiotics. To determine resistance genotype, quantitative PCR (qPCR) was performed from rectal swabs for 87 established resistance genes. Within-individual changes in antimicrobial resistance were calculated based on culture and qPCR results and correlated with exposure to relevant antibiotics (e.g., did β-lactam antibiotic exposure associate with a detectable change in β-lactam resistance over this 72-h period?). RESULTS Of 48 ICU patients, 41 (85%) received antibiotics. Overall, there was no increase in the antimicrobial resistance profile of colonizing gut bacteria during the 72-h study period. There was also no increase in antimicrobial resistance after stratification by receipt of antibiotics (i.e., no detectable increase in β-lactam, vancomycin, or macrolide resistance regardless of whether patients received those same antibiotics). This was true for both culture and PCR. Antimicrobial resistance pattern at ICU admission strongly predicted resistance pattern after 72 h. CONCLUSIONS Short-course ICU antibiotics made little detectable difference in the antimicrobial resistance pattern of colonizing gut bacteria over 72 h in the ICU. This provides an improved understanding of the dynamics of antimicrobial resistance in the ICU and some reassurance that short-course antibiotics may not adversely impact the stewardship goal of reducing antimicrobial resistance.
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Affiliation(s)
- Christian Munck
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA.
| | - Ravi U Sheth
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA
| | - Edward Cuaresma
- Department of Medicine, Columbia University Irving Medical Center, New York, USA
| | - Jessica Weidler
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Stephania L Stump
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Philip Zachariah
- Division of Pediatric Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - David H Chong
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Julian A Abrams
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, 630 West 168th Street, P&S 3-401, New York, NY, 10032, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA
| | - Daniel E Freedberg
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, 630 West 168th Street, P&S 3-401, New York, NY, 10032, USA.
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Abstract
Antimicrobial de-escalation (ADE) is a component of antimicrobial stewardship (AMS) aimed to reduce exposure to broad-spectrum antimicrobials. In the intensive care unit, ADE is a strong recommendation that is moderately applied in clinical practice. Following a systematic review of the literature, we assessed the studies identified on the topic which included one randomized controlled trial and 20 observational studies. The literature shows a low level of evidence, although observational studies suggested that this procedure is safe. The effects of ADE on the level of resistance of ecological systems and especially on the microbiota are unclear. The reviewers recommend de-escalating antimicrobial treatment in patients requiring long-term antibiotic therapy and considering de-escalation in short-term treatments.
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80
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Antibiotic modification versus withhold in febrile patients without evidence of bacterial infection, unresponsive to initial empiric regimen: a multicentre retrospective study conducted in Israel. Eur J Clin Microbiol Infect Dis 2020; 39:2027-2035. [PMID: 32572653 DOI: 10.1007/s10096-020-03957-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/16/2020] [Indexed: 10/23/2022]
Abstract
Prescribing antibiotics for febrile patients without proof of bacterial infection contributes to antimicrobial resistance. Lack of clinical response in these patients often leads to antibiotic escalation, although data supporting this strategy are scarce. This study compared outcomes of modifying, withholding, or continuing the same antibiotic regimen for such patients. Febrile or hypothermic stable patients with suspected infection, unresponsive to empiric antibiotic treatment, admitted to one of 15 internal medicine departments in three hospitals during a 5-year study period, were included. Patients with a definitive clinical or microbiological bacterial infection, malignancy, immunodeficiency, altered mental status, or need for mechanical ventilation were excluded. Participants were divided into groups based on treatment strategy determined 72 h after antibiotic initiation: antibiotic modified, withheld or continued. Outcomes measured included in-hospital and 30-day post-discharge-mortality rates, length of hospital stay (LOS) and days of antimicrobial therapy (DOT). A total of 486 patients met the inclusion criteria: 124 in the Antibiotic modified group, 67 in the Antibiotic withheld group and 295 in the Initial antibiotic continued group. Patient characteristics were similar among groups with no differences in mortality rates in-hospital (23% vs. 25% vs. 20%, p = 0.58) and within 30 days after discharge (5% vs. 3% vs. 4%, p = 0.83). Changing antibiotics led to longer LOS (9.0 ± 6.8 vs. 6.2 ± 5.6 days, p = 0.003) and more DOT (8.6 ± 6.0 vs. 3.2 ± 1.0 days, p < 0.001) compared to withholding treatment. Withholding as compared to modifying antibiotics, in febrile patients with no clear evidence of bacterial infection, is a safe strategy associated with decreased LOS and DOT.
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81
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Haudum C, Lindheim L, Ascani A, Trummer C, Horvath A, Münzker J, Obermayer-Pietsch B. Impact of Short-Term Isoflavone Intervention in Polycystic Ovary Syndrome (PCOS) Patients on Microbiota Composition and Metagenomics. Nutrients 2020; 12:E1622. [PMID: 32492805 PMCID: PMC7656308 DOI: 10.3390/nu12061622] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Polycystic ovary syndrome (PCOS) affects 5-20% of women of reproductive age worldwide and is associated with disorders of glucose metabolism. Hormone and metabolic signaling may be influenced by phytoestrogens, such as isoflavones. Their endocrine effects may modify symptom penetrance in PCOS. Equol is one of the most active isoflavone metabolites, produced by intestinal bacteria, and acts as a selective estrogen receptor modulator. METHOD In this interventional study of clinical and biochemical characterization, urine isoflavone levels were measured in PCOS and control women before and three days after a defined isoflavone intervention via soy milk. In this interventional study, bacterial equol production was evaluated using the log(equol: daidzein ratio) and microbiome, metabolic, and predicted metagenome analyses were performed. RESULTS After isoflavone intervention, predicted stool metagenomic pathways, microbial alpha diversity, and glucose homeostasis in PCOS improved resembling the profile of the control group at baseline. In the whole cohort, larger equol production was associated with lower androgen as well as fertility markers. CONCLUSION The dynamics in our metabolic, microbiome, and predicted metagenomic profiles underline the importance of external phytohormones on PCOS characteristics and a potential therapeutic approach or prebiotic in the future.
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Affiliation(s)
- Christoph Haudum
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Medical University Graz, 8010 Graz, Austria; (L.L.); (A.A.); (C.T.); (J.M.); (B.O.-P.)
- Center for Biomarker Research in Medicine (CBmed), 8010 Graz, Austria
| | - Lisa Lindheim
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Medical University Graz, 8010 Graz, Austria; (L.L.); (A.A.); (C.T.); (J.M.); (B.O.-P.)
| | - Angelo Ascani
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Medical University Graz, 8010 Graz, Austria; (L.L.); (A.A.); (C.T.); (J.M.); (B.O.-P.)
| | - Christian Trummer
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Medical University Graz, 8010 Graz, Austria; (L.L.); (A.A.); (C.T.); (J.M.); (B.O.-P.)
| | - Angela Horvath
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University Graz, 8010 Graz, Austria;
| | - Julia Münzker
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Medical University Graz, 8010 Graz, Austria; (L.L.); (A.A.); (C.T.); (J.M.); (B.O.-P.)
- Department of Medicine, Integrated Research and Treatment Centre for Adiposity Diseases, University of Leipzig, 04103 Leipzig, Germany
| | - Barbara Obermayer-Pietsch
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Medical University Graz, 8010 Graz, Austria; (L.L.); (A.A.); (C.T.); (J.M.); (B.O.-P.)
- Center for Biomarker Research in Medicine (CBmed), 8010 Graz, Austria
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82
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Kovtun AS, Averina OV, Alekseeva MG, Danilenko VN. Antibiotic Resistance Genes in the Gut Microbiota of Children with Autistic Spectrum Disorder as Possible Predictors of the Disease. Microb Drug Resist 2020; 26:1307-1320. [PMID: 31916894 DOI: 10.1089/mdr.2019.0325] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota (GM), which contains thousands of bacterial species, is a reservoir of antibiotic resistance genes (ARGs) called resistome. Early life exposure to antibiotics alters significantly the composition and function of the gut microbiota of children, which may trigger symptoms of autism spectrum disorder (ASD). This is because the GM plays an important role in the bidirectional communication between the gut and the brain and influences the brain normal functioning through multiple pathways. The goal of this article is to study the distribution of ARGs in the GM of 3- to 5-year-old healthy children and children with ASD living in Moscow, Russia. The metagenomic analysis of samples from both groups revealed differences in the signatures between them. The signatures consisted of the bacterial genera and aminoglycoside, β-lactam, macrolide, and tetracycline resistance genes that they harbored. Our results show an increase in ARGs in the resistome of the GM of children with ASD. These findings emphasize the negative influence of early-life antibiotic therapy. We found three ARGs, aac(6')-aph(2''), cepA-49, and tet(40), which could serve as markers of ASD. The additional functions carried out by the enzymes, encoded by these genes, are being discussed.
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Affiliation(s)
- Alexey S Kovtun
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology (State University), Moscow Oblast, Russia
| | - Olga V Averina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maria G Alekseeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Valery N Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology (State University), Moscow Oblast, Russia
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Willmann M, Vehreschild MJGT, Biehl LM, Vogel W, Dörfel D, Hamprecht A, Seifert H, Autenrieth IB, Peter S. Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study. BMC Biol 2019; 17:76. [PMID: 31533707 PMCID: PMC6749691 DOI: 10.1186/s12915-019-0692-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The selection pressure exercised by antibiotic drugs is an important consideration for the wise stewardship of antimicrobial treatment programs. Treatment decisions are currently based on crude assumptions, and there is an urgent need to develop a more quantitative knowledge base that can enable predictions of the impact of individual antibiotics on the human gut microbiome and resistome. RESULTS Using shotgun metagenomics, we quantified changes in the gut microbiome in two cohorts of hematological patients receiving prophylactic antibiotics; one cohort was treated with ciprofloxacin in a hospital in Tübingen and the other with cotrimoxazole in a hospital in Cologne. Analyzing this rich longitudinal dataset, we found that gut microbiome diversity was reduced in both treatment cohorts to a similar extent, while effects on the gut resistome differed. We observed a sharp increase in the relative abundance of sulfonamide antibiotic resistance genes (ARGs) by 148.1% per cumulative defined daily dose of cotrimoxazole in the Cologne cohort, but not in the Tübingen cohort treated with ciprofloxacin. Through multivariate modeling, we found that factors such as individual baseline microbiome, resistome, and plasmid diversity; liver/kidney function; and concurrent medication, especially virostatic agents, influence resistome alterations. Strikingly, we observed different effects on the plasmidome in the two treatment groups. There was a substantial increase in the abundance of ARG-carrying plasmids in the cohort treated with cotrimoxazole, but not in the cohort treated with ciprofloxacin, indicating that cotrimoxazole might contribute more efficiently to the spread of resistance. CONCLUSIONS Our study represents a step forward in developing the capability to predict the effect of individual antimicrobials on the human microbiome and resistome. Our results indicate that to achieve this, integration of the individual baseline microbiome, resistome, and mobilome status as well as additional individual patient factors will be required. Such personalized predictions may in the future increase patient safety and reduce the spread of resistance. TRIAL REGISTRATION ClinicalTrials.gov, NCT02058888 . Registered February 10 2014.
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Affiliation(s)
- Matthias Willmann
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.
| | - Maria J G T Vehreschild
- 1st Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Lena M Biehl
- 1st Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Wichard Vogel
- Medical Center, Department of Hematology, Oncology, Immunology, Rheumatology & Pulmonology, University of Tübingen, Tübingen, Germany
| | - Daniela Dörfel
- Medical Center, Department of Hematology, Oncology, Immunology, Rheumatology & Pulmonology, University of Tübingen, Tübingen, Germany
| | - Axel Hamprecht
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
| | - Harald Seifert
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
| | - Ingo B Autenrieth
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
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