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Sardzikova S, Andrijkova K, Svec P, Beke G, Klucar L, Minarik G, Bielik V, Kolenova A, Soltys K. Gut diversity and the resistome as biomarkers of febrile neutropenia outcome in paediatric oncology patients undergoing hematopoietic stem cell transplantation. Sci Rep 2024; 14:5504. [PMID: 38448687 PMCID: PMC10918076 DOI: 10.1038/s41598-024-56242-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/04/2024] [Indexed: 03/08/2024] Open
Abstract
The gut microbiota of paediatric oncology patients undergoing a conditioning regimen before hematopoietic stem cell transplantation is recently considered to play role in febrile neutropenia. Disruption of commensal microbiota and evolution of opportune pathogens community carrying a plethora of antibiotic-resistance genes play crucial role. However, the impact, predictive role and association of patient´s gut resistome in the course of the therapy is still to be elucidated. We analysed gut microbiota composition and resistome of 18 paediatric oncology patients undergoing hematopoietic stem cell transplantation, including 12 patients developing febrile neutropenia, hospitalized at The Bone Marrow Transplantation Unit of the National Institute of Children´s disease in Slovak Republic and healthy individuals (n = 14). Gut microbiome of stool samples obtained in 3 time points, before hematopoietic stem cell transplantation (n = 16), one week after hematopoietic stem cell transplantation (n = 16) and four weeks after hematopoietic stem cell transplantation (n = 14) was investigated using shotgun metagenome sequencing and bioinformatical analysis. We identified significant decrease in alpha-diversity and nine antibiotic-resistance genes msr(C), dfrG, erm(T), VanHAX, erm(B), aac(6)-aph(2), aph(3)-III, ant(6)-Ia and aac(6)-Ii, one week after hematopoietic stem cell transplantation associated with febrile neutropenia. Multidrug-resistant opportune pathogens of ESKAPE, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae and Escherichia coli found in the gut carried the significant subset of patient's resistome. Over 50% of patients treated with trimethoprim/sulfamethoxazole, piperacillin/tazobactam and amikacin carried antibiotic-resistance genes to applied treatment. The alpha diversity and the resistome of gut microbiota one week after hematopoietic stem cell transplantation is relevant predictor of febrile neutropenia outcome after hematopoietic stem cell transplantation. Furthermore, the interindividual diversity of multi-drug resistant opportunistic pathogens with variable portfolios of antibiotic-resistance genes indicates necessity of preventive, personalized approach.
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Affiliation(s)
- Sara Sardzikova
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Kristina Andrijkova
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Peter Svec
- Department of Paediatric Haematology and Oncology, Children's Haematology and Oncology Clinic and Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | - Gabor Beke
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lubos Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Viktor Bielik
- Department of Biological and Medical Science, Faculty of Physical Education and Sport, Comenius University in Bratislava, Bratislava, Slovakia
| | - Alexandra Kolenova
- Department of Paediatric Haematology and Oncology, Children's Haematology and Oncology Clinic and Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katarina Soltys
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
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Elgarten CW, Margolis EB, Kelly MS. The Microbiome and Pediatric Transplantation. J Pediatric Infect Dis Soc 2024; 13:S80-S89. [PMID: 38417089 PMCID: PMC10901476 DOI: 10.1093/jpids/piad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/25/2023] [Indexed: 03/01/2024]
Abstract
The microbial communities that inhabit our bodies have been increasingly linked to host physiology and pathophysiology. This microbiome, through its role in colonization resistance, influences the risk of infections after transplantation, including those caused by multidrug-resistant organisms. In addition, through both direct interactions with the host immune system and via the production of metabolites that impact local and systemic immunity, the microbiome plays an important role in the establishment of immune tolerance after transplantation, and conversely, in the development of graft-versus-host disease and graft rejection. This review offers a comprehensive overview of the evidence for the role of the microbiome in hematopoietic cell and solid organ transplant complications, drivers of microbiome shift during transplantation, and the potential of microbiome-based therapies to improve pediatric transplantation outcomes.
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Affiliation(s)
- Caitlin W Elgarten
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elisa B Margolis
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Pediatrics, University of Tennessee Health Sciences Center, Memphis, Tennessee, USA
| | - Matthew S Kelly
- Departments of Pediatrics and Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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3
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Heston SM, Young RR, Jenkins K, Martin PL, Stokhuyzen A, Ward DV, Bhattarai SK, Bucci V, Arshad M, Chao NJ, Seed PC, Kelly MS. The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children. Gut Microbes 2024; 16:2333748. [PMID: 38555499 PMCID: PMC10984140 DOI: 10.1080/19490976.2024.2333748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
Antibiotic resistance is a global threat driven primarily by antibiotic use. We evaluated the effects of antibiotic exposures on the gut microbiomes and resistomes of children at high risk of colonization by antibiotic-resistant bacteria. We performed shotgun metagenomic sequencing of 691 serially collected fecal samples from 80 children (<18 years) undergoing hematopoietic cell transplantation. We evaluated the effects of aerobic (cefepime, vancomycin, fluoroquinolones, aminoglycosides, macrolides, and trimethoprim-sulfamethoxazole) and anaerobic (piperacillin-tazobactam, carbapenems, metronidazole, and clindamycin) antibiotic exposures on the diversity and composition of the gut microbiome and resistome. We identified 372 unique antibiotic resistance genes (ARGs); the most frequent ARGs identified encode resistance to tetracyclines (n = 88), beta-lactams (n = 84), and fluoroquinolones (n = 79). Both aerobic and anaerobic antibiotic exposures were associated with a decrease in the number of bacterial species (aerobic, β = 0.71, 95% CI: 0.64, 0.79; anaerobic, β = 0.66, 95% CI: 0.53, 0.82) and the number of unique ARGs (aerobic, β = 0.81, 95% CI: 0.74, 0.90; anaerobic, β = 0.73, 95% CI: 0.61, 0.88) within the gut metagenome. However, only antibiotic regimens that included anaerobic activity were associated with an increase in acquisition of new ARGs (anaerobic, β = 1.50; 95% CI: 1.12, 2.01) and an increase in the relative abundance of ARGs in the gut resistome (anaerobic, β = 1.62; 95% CI: 1.15, 2.27). Specific antibiotic exposures were associated with distinct changes in the number and abundance of ARGs for individual antibiotic classes. Our findings detail the impact of antibiotics on the gut microbiome and resistome and demonstrate that anaerobic antibiotics are particularly likely to promote acquisition and expansion of antibiotic-resistant bacteria.
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Affiliation(s)
- Sarah M. Heston
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Rebecca R. Young
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Insitute, Duke University School of Medicine, Durham, NC, USA
| | - Kirsten Jenkins
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Paul L. Martin
- Division of Pediatric Transplant and Cellular Therapy, Duke University School of Medicine, Durham, NC, USA
| | - Andre Stokhuyzen
- Division of Pediatric Transplant and Cellular Therapy, Duke University School of Medicine, Durham, NC, USA
| | - Doyle V. Ward
- Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shakti K. Bhattarai
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mehreen Arshad
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Nelson J. Chao
- Division of Hematologic Malignancies and Cellular Therapy, Duke University School of Medicine, Durham, NC, USA
| | - Patrick C. Seed
- Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
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Sardzikova S, Andrijkova K, Svec P, Beke G, Klucar L, Minarik G, Bielik V, Kolenova A, Soltys K. High Diversity but Monodominance of Multidrug-Resistant Bacteria in Immunocompromised Pediatric Patients with Acute Lymphoblastic Leukemia Developing GVHD Are Not Associated with Changes in Gut Mycobiome. Antibiotics (Basel) 2023; 12:1667. [PMID: 38136701 PMCID: PMC10740403 DOI: 10.3390/antibiotics12121667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/15/2023] [Accepted: 11/18/2023] [Indexed: 12/24/2023] Open
Abstract
Graft-versus-host disease (GvHD) is a severe complication after hematopoietic stem cell transplantation (HSCT). Our study focused on identifying multidrug-resistant (MDR) gut bacteria associated with GvHD-prone guts and association with gut microbiota (GM) diversity, bacteriome, and mycobiome composition in post-HSCT patients. We examined 11 pediatric patients with acute lymphoblastic leukemia (ALL), including six with GvHD, within three time points: seven days pre-HSCT, seven days post-, and 28 days post-HSCT. The gut microbiome and its resistome were investigated using metagenomic sequencing, taxonomically classified with Kraken2, and statistically evaluated for significance using appropriate tests. We observed an increase in the abundance of MDR bacteria, mainly Enterococcus faecium strains carrying msr(C), erm(T), aac(6')-li, dfrG, and ant(6)-la genes, in GvHD patients one week post-HSCT. Conversely, non-GvHD patients had more MDR beneficial bacteria pre-HSCT, promoting immunosurveillance, with resistance genes increasing one-month post-HSCT. MDR beneficial bacteria included the anti-inflammatory Bacteroides fragilis, Ruminococcus gnavus, and Turicibacter, while most MDR bacteria represented the dominant species of GM. Changes in the gut mycobiome were not associated with MDR bacterial monodominance or GvHD. Significant α-diversity decline (Shannon index) one week and one month post-HSCT in GvHD patients (p < 0.05) was accompanied by increased Pseudomonadota and decreased Bacteroidota post-HSCT. Our findings suggest that MDR commensal gut bacteria may preserve diversity and enhance immunosurveillance, potentially preventing GvHD in pediatric ALL patients undergoing HSCT. This observation has therapeutic implications.
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Affiliation(s)
- Sara Sardzikova
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Kristina Andrijkova
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Peter Svec
- Department of Pediatric Hematology and Oncology, Children’s Haematology and Oncology Clinic, Faculty of Medicine, Comenius University in Bratislava, 833 40 Bratislava, Slovakia
| | - Gabor Beke
- Institute of Molecular Biology, Slovak Academy of Sciences, 841 04 Bratislava, Slovakia
| | - Lubos Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, 841 04 Bratislava, Slovakia
| | - Gabriel Minarik
- Medirex Group Academy n.p.o., Novozamocka 67, 949 05 Nitra, Slovakia
| | - Viktor Bielik
- Department of Biological and Medical Science, Faculty of Physical Education and Sport, Comenius University in Bratislava, 814 69 Bratislava, Slovakia
| | - Alexandra Kolenova
- Department of Pediatric Hematology and Oncology, Children’s Haematology and Oncology Clinic, Faculty of Medicine, Comenius University in Bratislava, 833 40 Bratislava, Slovakia
| | - Katarina Soltys
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
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Masetti R, Leardini D, Muratore E, Fabbrini M, D’Amico F, Zama D, Baccelli F, Gottardi F, Belotti T, Ussowicz M, Fraczkiewicz J, Cesaro S, Zecca M, Merli P, Candela M, Pession A, Locatelli F, Prete A, Brigidi P, Turroni S. Gut microbiota diversity before allogeneic hematopoietic stem cell transplantation as a predictor of mortality in children. Blood 2023; 142:1387-1398. [PMID: 37856089 PMCID: PMC10651870 DOI: 10.1182/blood.2023020026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/16/2023] [Indexed: 10/20/2023] Open
Abstract
The correlation existing between gut microbiota diversity and survival after allogeneic hematopoietic stem cell transplantation (allo-HSCT) has so far been studied in adults. Pediatric studies question whether this association applies to children as well. Stool samples from a multicenter cohort of 90 pediatric allo-HSCT recipients were analyzed using 16S ribosomal RNA amplicon sequencing to profile the gut microbiota and estimate diversity with the Shannon index. A global-to-local networking approach was used to characterize the ecological structure of the gut microbiota. Patients were stratified into higher- and lower-diversity groups at 2 time points: before transplantation and at neutrophil engraftment. The higher-diversity group before transplantation exhibited a higher probability of overall survival (88.9% ± 5.7% standard error [SE] vs 62.7% ± 8.2% SE; P = .011) and lower incidence of grade 2 to 4 and grade 3 to 4 acute graft-versus-host disease (aGVHD). No significant difference in relapse-free survival was observed between the 2 groups (80.0% ± 6.0% SE vs 55.4% ± 10.8% SE; P = .091). The higher-diversity group was characterized by higher relative abundances of potentially health-related microbial families, such as Ruminococcaceae and Oscillospiraceae. In contrast, the lower-diversity group showed an overabundance of Enterococcaceae and Enterobacteriaceae. Network analysis detected short-chain fatty acid producers, such as Blautia, Faecalibacterium, Roseburia, and Bacteroides, as keystones in the higher-diversity group. Enterococcus, Escherichia-Shigella, and Enterobacter were instead the keystones detected in the lower-diversity group. These results indicate that gut microbiota diversity and composition before transplantation correlate with survival and with the likelihood of developing aGVHD.
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Affiliation(s)
- Riccardo Masetti
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Davide Leardini
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Edoardo Muratore
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Marco Fabbrini
- Department of Medical and Surgical Sciences, Microbiomics Unit, University of Bologna, Bologna, Italy
- Department of Pharmacy and Biotechnology, Unit of Microbiome Science and Biotechnology, University of Bologna, Bologna, Italy
| | - Federica D’Amico
- Department of Medical and Surgical Sciences, Microbiomics Unit, University of Bologna, Bologna, Italy
| | - Daniele Zama
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Pediatric Emergency Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Francesco Baccelli
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Francesca Gottardi
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tamara Belotti
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Marek Ussowicz
- Department and Clinic of Pediatric Oncology, Hematology and Bone Marrow Transplantation, Wrocław Medical University, Wrocław, Poland
| | - Jowita Fraczkiewicz
- Department and Clinic of Pediatric Oncology, Hematology and Bone Marrow Transplantation, Wrocław Medical University, Wrocław, Poland
| | - Simone Cesaro
- Department of Mother and Child, Pediatric Hematology Oncology Unit, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Marco Zecca
- Pediatric Hematology/Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Pietro Merli
- Department of Pediatric Hematology and Oncology, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, Unit of Microbiome Science and Biotechnology, University of Bologna, Bologna, Italy
| | - Andrea Pession
- Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
- Catholic University of the Sacred Heart, Rome, Italy
| | - Arcangelo Prete
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, Microbiomics Unit, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, Unit of Microbiome Science and Biotechnology, University of Bologna, Bologna, Italy
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Pharmacomicrobiomics in Pediatric Oncology: The Complex Interplay between Commonly Used Drugs and Gut Microbiome. Int J Mol Sci 2022; 23:ijms232315387. [PMID: 36499714 PMCID: PMC9740824 DOI: 10.3390/ijms232315387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/27/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome (GM) has emerged in the last few years as a main character in several diseases. In pediatric oncological patients, GM has a role in promoting the disease, modulating the effectiveness of therapies, and determining the clinical outcomes. The therapeutic course for most pediatric cancer influences the GM due to dietary modifications and several administrated drugs, including chemotherapies, antibiotics and immunosuppressants. Interestingly, increasing evidence is uncovering a role of the GM on drug pharmacokinetics and pharmacodynamics, defining a bidirectional relationship. Indeed, the pediatric setting presents some contrasts with respect to the adult, since the GM undergoes a constant multifactorial evolution during childhood following external stimuli (such as diet modification during weaning). In this review, we aim to summarize the available evidence of pharmacomicrobiomics in pediatric oncology.
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Leardini D, Muratore E, Abram N, Baccelli F, Belotti T, Prete A, Gori D, Masetti R. Effectiveness of Quinolone Prophylaxis in Pediatric Acute Leukemia and Hematopoietic Stem Cell Transplantation: A Systematic Review and Meta-analysis. Open Forum Infect Dis 2022; 9:ofac594. [PMID: 36504701 PMCID: PMC9728521 DOI: 10.1093/ofid/ofac594] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
The effectiveness of quinolone prophylaxis in high-risk hematological pediatric patients is controversial. A systematic review was performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, including studies that involved children and young adults undergoing chemotherapy for acute leukemia or hematopoietic stem cell transplantation (HSCT) who received quinolone prophylaxis compared with no prophylaxis. A meta-analysis was performed on bloodstream infections and neutropenic fever. Data regarding the impact of prophylaxis on overall survival, antibiotic exposure, antibiotic-related adverse effects, antibiotic resistance, Clostridium difficile infections, fungal infections, length of hospitalization, and costs were reviewed in the descriptive analysis. Sixteen studies were included in the qualitative analysis, and 10 of them met the criteria for quantitative analysis. Quinolone prophylaxis was effective in reducing the rate of bloodstream infections and neutropenic fever in pediatric acute leukemia compared with no prophylaxis, but it had no significant effect in HSCT recipients. Prophylaxis was associated with a higher rate of bacterial resistance to fluoroquinolones and higher antibiotic exposure.
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Affiliation(s)
| | | | - Nicoletta Abram
- Pediatric Oncology and Hematology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Francesco Baccelli
- Correspondence: F. Baccelli, MD, Pediatric Oncology and Hematology Unit “Lalla Seràgnoli,” Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Ospedale Policlinico S. Orsola-Malpighi, Via Massarenti 11, 40138 Bologna, Italy ()
| | - Tamara Belotti
- Pediatric Oncology and Hematology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Arcangelo Prete
- Pediatric Oncology and Hematology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Davide Gori
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
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8
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Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults. Nat Commun 2022; 13:586. [PMID: 35102136 PMCID: PMC8803835 DOI: 10.1038/s41467-022-28048-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022] Open
Abstract
Bacterial bloodstream infections are a major cause of morbidity and mortality among patients undergoing hematopoietic cell transplantation (HCT). Although previous research has demonstrated that pathogens may translocate from the gut microbiome into the bloodstream to cause infections, the mechanisms by which HCT patients acquire pathogens in their microbiome have not yet been described. Here, we use linked-read and short-read metagenomic sequencing to analyze 401 stool samples collected from 149 adults undergoing HCT and hospitalized in the same unit over three years, many of whom were roommates. We use metagenomic assembly and strain-specific comparison methods to search for high-identity bacterial strains, which may indicate transmission between the gut microbiomes of patients. Overall, the microbiomes of patients who share time and space in the hospital do not converge in taxonomic composition. However, we do observe six pairs of patients who harbor identical or nearly identical strains of the pathogen Enterococcus faecium, or the gut commensals Akkermansia muciniphila and Hungatella hathewayi. These shared strains may result from direct transmission between patients who shared a room and bathroom, acquisition from a common hospital source, or transmission from an unsampled intermediate. We also identify multiple patients with identical strains of species commonly found in commercial probiotics, including Lactobacillus rhamnosus and Streptococcus thermophilus. In summary, our findings indicate that sharing of identical pathogens between the gut microbiomes of multiple patients is a rare phenomenon. Furthermore, the observed potential transmission of commensal, immunomodulatory microbes suggests that exposure to other humans may contribute to microbiome reassembly post-HCT. Here, Siranosian et al. provide evidence for rare transmission of commensal and pathogenic bacteria between the microbiomes of hospitalized adults, with important factors being roommate overlap and exposure to broad-spectrum antibiotics.
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Gut microbiome in pediatric acute leukemia: from predisposition to cure. Blood Adv 2021; 5:4619-4629. [PMID: 34610115 PMCID: PMC8759140 DOI: 10.1182/bloodadvances.2021005129] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/25/2021] [Indexed: 01/02/2023] Open
Abstract
The gut microbiome (GM) has emerged as a key factor in the genesis and progression of many diseases. The intestinal bacterial composition also influences treatment-related side effects and even the efficacy of oncological therapies. Acute leukemia (AL) is the most common cancer among children and the most frequent cause of cancer-related death during childhood. Outcomes have improved considerably over the past 4 decades, with the current long-term survival for acute lymphoblastic leukemia being ∼90%. However, several acute toxicities and long-term sequelae are associated with the multimodal therapy protocols applied in these patients. Specific GM configurations could contribute to the multistep developmental hypothesis for leukemogenesis. Moreover, GM alterations occur during the AL therapeutic course and are associated with treatment-related complications, especially during hematopoietic stem cell transplantation. The GM perturbation could last even after the removal of microbiome-modifying factors, like antibiotics, chemotherapeutic drugs, or alloimmune reactions, contributing to several health-related issues in AL survivors. The purpose of this article is to provide a comprehensive review of the chronological changes of GM in children with AL, from predisposition to cure. The underpinning biological processes and the potential interventions to modulate the GM toward a potentially health-promoting configuration are also highlighted.
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10
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Tavella T, Turroni S, Brigidi P, Candela M, Rampelli S. The Human Gut Resistome up to Extreme Longevity. mSphere 2021; 6:e0069121. [PMID: 34494880 PMCID: PMC8550338 DOI: 10.1128/msphere.00691-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/26/2022] Open
Abstract
Antibiotic resistance (AR) is indisputably a major health threat which has drawn much attention in recent years. In particular, the gut microbiome has been shown to act as a pool of AR genes, potentially available to be transferred to opportunistic pathogens. Herein, we investigated for the first time changes in the human gut resistome during aging, up to extreme longevity, by analyzing shotgun metagenomics data of fecal samples from a geographically defined cohort of 62 urban individuals, stratified into four age groups: young adults, elderly, centenarians, and semisupercentenarians, i.e., individuals aged up to 109 years. According to our findings, some AR genes are similarly represented in all subjects regardless of age, potentially forming part of the core resistome. Interestingly, aging was found to be associated with a higher burden of some AR genes, including especially proteobacterial genes encoding multidrug efflux pumps. Our results warn of possible health implications and pave the way for further investigations aimed at containing AR accumulation, with the ultimate goal of promoting healthy aging. IMPORTANCE Antibiotic resistance is widespread among different ecosystems, and in humans it plays a key role in shaping the composition of the gut microbiota, enhancing the ecological fitness of certain bacterial populations when exposed to antibiotics. A considerable component of the definition of healthy aging and longevity is associated with the structure of the gut microbiota, and, in this regard, the presence of antibiotic-resistant bacteria is critical to many pathologies that come about with aging. However, the structure of the resistome has not yet been sufficiently elucidated. Here, we show distinct antibiotic resistance assets and specific microbial consortia characterizing the human gut resistome through aging.
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Affiliation(s)
- Teresa Tavella
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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11
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Early modifications of the gut microbiome in children with hepatic sinusoidal obstruction syndrome after hematopoietic stem cell transplantation. Sci Rep 2021; 11:14307. [PMID: 34253759 PMCID: PMC8275574 DOI: 10.1038/s41598-021-93571-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/25/2021] [Indexed: 01/04/2023] Open
Abstract
Hepatic sinusoidal obstruction syndrome (SOS/VOD) represents a dramatic complication of hematopoietic stem cell transplantation (HSCT), particularly in children. Recent evidence has suggested a role for the gut microbiome (GM) in the context of HSCT and its related complications, but no data are available on the relationship between GM and SOS/VOD. Here, we conducted a retrospective case–control study in allo-HSCT pediatric patients developing or not SOS/VOD and profiled their GM over time, from before the transplant up to 72 days after. A rich and diverse GM before HSCT was found to be associated with a reduced likelihood of developing SOS/VOD. Furthermore, prior to transplant, patients not developing SOS/VOD showed an enrichment in some typically health-associated commensals, such as Bacteroides, Ruminococcaceae and Lachnospiraceae. Their levels remained overall higher until post-transplant. This high-diversity configuration resembles that described in other studies for other HSCT-related complications, including graft-versus-host disease, potentially representing a common protective GM feature against HSCT complications.
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12
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García-Bayona L, Coyne MJ, Comstock LE. Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering. PLoS Genet 2021; 17:e1009541. [PMID: 33901198 PMCID: PMC8102008 DOI: 10.1371/journal.pgen.1009541] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/06/2021] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is a dense microbial ecosystem with extensive opportunities for bacterial contact-dependent processes such as conjugation and Type VI secretion system (T6SS)-dependent antagonism. In the gut Bacteroidales, two distinct genetic architectures of T6SS loci, GA1 and GA2, are contained on Integrative and Conjugative Elements (ICE). Despite intense interest in the T6SSs of the gut Bacteroidales, there is only a superficial understanding of their evolutionary patterns, and of their dissemination among Bacteroidales species in human gut communities. Here, we combine extensive genomic and metagenomic analyses to better understand their ecological and evolutionary dynamics. We identify new genetic subtypes, document extensive intrapersonal transfer of these ICE to Bacteroidales species within human gut microbiomes, and most importantly, reveal frequent population fixation of these newly armed strains in multiple species within a person. We further show the distribution of each of the distinct T6SSs in human populations and show there is geographical clustering. We reveal that the GA1 T6SS ICE integrates at a minimal recombination site leading to their integration throughout genomes and their frequent interruption of genes, whereas the GA2 T6SS ICE integrate at one of three different tRNA genes. The exclusion of concurrent GA1 and GA2 T6SSs in individual strains is associated with intact T6SS loci and with an ICE-encoded gene. By performing a comprehensive analysis of mobile genetic elements (MGE) in co-resident Bacteroidales species in numerous human gut communities, we identify 74 MGE that transferred to multiple Bacteroidales species within individual gut microbiomes. We further show that only three other MGE demonstrate multi-species spread in human gut microbiomes to the degree demonstrated by the GA1 and GA2 ICE. These data underscore the ubiquity and dissemination of mobile T6SS loci within Bacteroidales communities and across human populations.
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Affiliation(s)
- Leonor García-Bayona
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael J. Coyne
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Laurie E. Comstock
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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13
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Pession A, Zama D, Muratore E, Leardini D, Gori D, Guaraldi F, Prete A, Turroni S, Brigidi P, Masetti R. Fecal Microbiota Transplantation in Allogeneic Hematopoietic Stem Cell Transplantation Recipients: A Systematic Review. J Pers Med 2021; 11:100. [PMID: 33557125 PMCID: PMC7913807 DOI: 10.3390/jpm11020100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/25/2021] [Accepted: 02/02/2021] [Indexed: 12/29/2022] Open
Abstract
The disruption of gut microbiota eubiosis has been linked to major complications in allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients. Various strategies have been developed to reduce dysbiosis and related complications. Fecal microbiota transplantation (FMT) consists of the infusion of fecal matter from a healthy donor to restore impaired intestinal homeostasis, and could be applied in the allo-HSCT setting. We conducted a systematic review of studies addressing the use of FMT in allo-HSCT patients. In the 23 papers included in the qualitative synthesis, FMT was used for the treatment of recurrent Clostridioides difficile infections or as a therapeutic strategy for steroid-resistant gut aGvHD. FMT was also performed with a preventive aim (e.g., to decolonize from antibiotic-resistant bacteria). Additional knowledge on the biological mechanisms underlying clinical findings is needed in order to employ FMT in clinical practice. There is also concern regarding the administration of microbial consortia in immune-compromised patients with altered gut permeability. Therefore, the safety profile and efficacy of the procedure must be determined to better assess the role of FMT in allo-HSCT recipients.
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Affiliation(s)
- Andrea Pession
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, Pediatric Unit—IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (A.P.); (D.Z.); (D.L.); (A.P.); (R.M.)
| | - Daniele Zama
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, Pediatric Unit—IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (A.P.); (D.Z.); (D.L.); (A.P.); (R.M.)
| | - Edoardo Muratore
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, Pediatric Unit—IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (A.P.); (D.Z.); (D.L.); (A.P.); (R.M.)
| | - Davide Leardini
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, Pediatric Unit—IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (A.P.); (D.Z.); (D.L.); (A.P.); (R.M.)
| | - Davide Gori
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, 40126 Bologna, Italy; (D.G.); (F.G.)
| | - Federica Guaraldi
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, 40126 Bologna, Italy; (D.G.); (F.G.)
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40126 Bologna, Italy
| | - Arcangelo Prete
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, Pediatric Unit—IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (A.P.); (D.Z.); (D.L.); (A.P.); (R.M.)
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy;
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy;
| | - Riccardo Masetti
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, Pediatric Unit—IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (A.P.); (D.Z.); (D.L.); (A.P.); (R.M.)
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14
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Bossù G, Di Sario R, Argentiero A, Esposito S. Antimicrobial Prophylaxis and Modifications of the Gut Microbiota in Children with Cancer. Antibiotics (Basel) 2021; 10:antibiotics10020152. [PMID: 33546312 PMCID: PMC7913491 DOI: 10.3390/antibiotics10020152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
In children with cancer, chemotherapy can produce cytotoxic effects, resulting in immunosuppression and an augmented risk of febrile neutropenia and bloodstream infections. This has led to widespread use of antibiotic prophylaxis which, combined with intensive chemotherapy treatment, could have a long-term effect on the gastrointestinal microbiome. In this review, we aimed to analyze the current literature about the widespread use of antibiotic prophylaxis in children experiencing infectious complications induced by chemotherapy and its effects on the gut microbiome. Our review of the literature shows that antimicrobial prophylaxis in children with cancer is still a trending topic and, at the moment, there are not enough data to define universal guidelines. Children with cancer experience long and painful medical treatments and side effects, which are associated with great economic and social burdens, important psychological consequences, and dysbiosis induced by antibiotics and also by chemotherapy. Considering the importance of a healthy gut microbiota, studies are needed to understand the impact of dysbiosis in response to therapy in these children and to define how to modulate the microbiome to favor a positive therapeutic outcome.
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15
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Masetti R, Zama D, Leardini D, Muratore E, Turroni S, Prete A, Brigidi P, Pession A. The gut microbiome in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation. Pediatr Blood Cancer 2020; 67:e28711. [PMID: 32939928 DOI: 10.1002/pbc.28711] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022]
Abstract
The gut microbiome (GM) has been associated with different clinical outcomes in the context of allogeneic hematopoietic stem cell transplantation (HSCT). Large multicenter cohort studies in adults have found significant correlations with overall survival, relapse, and incidence of complications. Moreover, GM is already a promising target for therapeutic interventions. However, few data are available in children, a population presenting unique features and challenges. During childhood, the GM evolves rapidly with large structural fluctuations, alongside with the maturation of the immune system. Furthermore, the HSCT procedure presents significant differences in children. These considerations underline the importance of a specific focus on the pediatric setting, and the role of GM and its age-dependent trajectory in influencing the immunity reconstitution and clinical outcomes. This review provides a comprehensive overview of the available evidence in the field of GM and pediatric HSCT, highlighting age-specific issues and discussing GM-based therapeutic approaches.
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Affiliation(s)
- Riccardo Masetti
- Pediatric Oncology and Hematology Unit "Lalla Seràgnoli," Department of Pediatrics, University of Bologna, Sant'Orsola Malpighi Hospital, Bologna, Italy
| | - Daniele Zama
- Pediatric Oncology and Hematology Unit "Lalla Seràgnoli," Department of Pediatrics, University of Bologna, Sant'Orsola Malpighi Hospital, Bologna, Italy
| | - Davide Leardini
- Pediatric Oncology and Hematology Unit "Lalla Seràgnoli," Department of Pediatrics, University of Bologna, Sant'Orsola Malpighi Hospital, Bologna, Italy
| | - Edoardo Muratore
- Pediatric Oncology and Hematology Unit "Lalla Seràgnoli," Department of Pediatrics, University of Bologna, Sant'Orsola Malpighi Hospital, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Arcangelo Prete
- Pediatric Oncology and Hematology Unit "Lalla Seràgnoli," Department of Pediatrics, University of Bologna, Sant'Orsola Malpighi Hospital, Bologna, Italy
| | - Patrizia Brigidi
- Department of Medicine and Surgery (DIMEC), University of Bologna, Bologna, Italy
| | - Andrea Pession
- Pediatric Oncology and Hematology Unit "Lalla Seràgnoli," Department of Pediatrics, University of Bologna, Sant'Orsola Malpighi Hospital, Bologna, Italy
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16
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Emergency Combination of Four Drugs for Bloodstream Infection Caused by Carbapenem-Resistant Enterobacteriaceae in Severe Agranulocytosis Patients with Hematologic Malignancies after Hematopoietic Stem Cell Transplantation. Emerg Med Int 2020; 2020:9358426. [PMID: 32832159 PMCID: PMC7424386 DOI: 10.1155/2020/9358426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/24/2020] [Accepted: 06/06/2020] [Indexed: 11/18/2022] Open
Abstract
Bloodstream infection (BSI) caused by multidrug-resistant (MDR) bacteria or extensively drug-resistant (XDR) bacteria is a global threat. However, an effective treatment regimen is still controversial and inadequate due to the rapid deterioration caused by the bacteria. In immunocompromised and neutropenic patients, MDR-BSI is an emergency, which causes treatment-related mortality. In this study, four agranulocytosis patients with hematologic malignancies after HSCT receiving treatment for carbapenem-resistant Enterobacteriaceae- (CRE-) BSI were included. Conventional treatment using two to three combined antibiotics was administered in the first and second patients. Combination treatment using four drugs, polymyxin B, high-dose tigecycline, fosfomycin, and double-dose carbapenem, was administered in the third and fourth patients. None of the patients receiving conventional treatment survived. Both patients receiving combination treatment using four drugs survived. Therefore, four-drug combination therapy may be needed in CRE-BSI patients who experienced severe agranulocytosis after HSCT. The efficacy of the four-drug combination treatment for CRE-BSI patients as well as the adverse effects need to be further studied.
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17
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Zama D, Bossù G, Leardini D, Muratore E, Biagi E, Prete A, Pession A, Masetti R. Insights into the role of intestinal microbiota in hematopoietic stem-cell transplantation. Ther Adv Hematol 2020; 11:2040620719896961. [PMID: 32010434 PMCID: PMC6974760 DOI: 10.1177/2040620719896961] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota (GM) is able to modulate the human immune system. The development of novel investigation methods has provided better characterization of the GM, increasing our knowledge of the role of GM in the context of hematopoietic stem-cell transplantation (HSCT). In particular, the GM influences the development of the major complications seen after HSCT, having an impact on overall survival. In fact, this evidence highlights the possible therapeutic implications of modulation of the GM during HSCT. Insights into the complex mechanisms and functions of the GM are essential for the rational design of these therapeutics. To date, preemptive and curative approaches have been tested. The current state of understanding of the impact of the GM on HSCT, and therapies targeting the GM balance is reviewed herein.
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Affiliation(s)
- Daniele Zama
- Pediatric Oncology and Hematology Unit ‘Lalla
Seràgnoli,’ Sant’Orsola-Malpighi Hospital, University of Bologna, Via
Massarenti 11, Bologna, 40137, Italy
| | - Gianluca Bossù
- Department of Pediatrics, ‘Lalla Seràgnoli,’
Hematology-Oncology Unit, University of Bologna, Italy
| | - Davide Leardini
- Department of Pediatrics, ‘Lalla Seràgnoli,’
Hematology-Oncology Unit, University of Bologna, Italy
| | - Edoardo Muratore
- Department of Pediatrics, ‘Lalla Seràgnoli,’
Hematology-Oncology Unit, University of Bologna, Italy
| | - Elena Biagi
- Department of Pharmacy and Biotechnology,
University of Bologna, Bologna, Italy
| | - Arcangelo Prete
- Department of Pediatrics, ‘Lalla Seràgnoli,’
Hematology-Oncology Unit, University of Bologna, Italy
| | - Andrea Pession
- Department of Pediatrics, ‘Lalla Seràgnoli,’
Hematology-Oncology Unit, University of Bologna, Italy
| | - Riccardo Masetti
- Department of Pediatrics, ‘Lalla Seràgnoli,’
Hematology-Oncology Unit, University of Bologna, Italy
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