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Seijas-Pereda L, Carmena D, Rescalvo-Casas C, Hernando-Gozalo M, Prieto-Pérez L, Cuadros-González J, Pérez-Tanoira R. Global Dynamics of Gastrointestinal Colonisations and Antimicrobial Resistance: Insights from International Travellers to Low- and Middle-Income Countries. Trop Med Infect Dis 2024; 9:182. [PMID: 39195620 PMCID: PMC11359149 DOI: 10.3390/tropicalmed9080182] [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: 07/11/2024] [Revised: 08/08/2024] [Accepted: 08/15/2024] [Indexed: 08/29/2024] Open
Abstract
Gastrointestinal microorganism resistance and dissemination are increasing, partly due to international travel. This study investigated gastrointestinal colonisations and the acquisition of antimicrobial resistance (AMR) genes among international travellers moving between Spain and low- and middle-income countries (Peru and Ethiopia). We analysed 102 stool samples from 51 volunteers collected before and after travel, revealing significantly higher rates of colonisation by both bacteria and protists upon return. Diarrhoeagenic strains of E. coli were the most notable microorganism detected using RT-PCR with the Seegene Allplex™ Gastrointestinal Panel Assays. A striking prevalence of β-lactamase resistance genes, particularly the TEM gene, was observed both before and after travel. No significant differences in AMR genes were found between the different locations. These findings highlight the need for rigorous surveillance and preventive strategies, as travel does not significantly impact AMR gene acquisition but does affect microbial colonisations. This study provides valuable insights into the intersection of gastrointestinal microorganism acquisition and AMR in international travellers, underscoring the need for targeted interventions and increased awareness.
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Affiliation(s)
- Laura Seijas-Pereda
- Department of Microbiology, Príncipe de Asturias Universitary Hospital, Carretera Alcalá-Meco s/n, 28805 Alcalá de Henares, Spain; (C.R.-C.); (M.H.-G.); (J.C.-G.); (R.P.-T.)
- Department of Biomedicine and Biotechnology, Faculty of Medicine, University of Alcalá, C/19 Av. De Madrid, 28871 Alcalá de Henares, Spain
| | - David Carmena
- Parasitology Reference and Research Laboratory, Spanish National Centre for Microbiology, Health Institute Carlos III. Ctra. De Pozuelo, 28, 28222 Majadahonda, Spain;
- Center for Biomedical Research Network (CIBER) in Infectious Diseases, Health Institute Carlos III. C/Merlchor Fernández Almagro, 3, Fuencarral-El Pardo, 28029 Madrid, Spain
| | - Carlos Rescalvo-Casas
- Department of Microbiology, Príncipe de Asturias Universitary Hospital, Carretera Alcalá-Meco s/n, 28805 Alcalá de Henares, Spain; (C.R.-C.); (M.H.-G.); (J.C.-G.); (R.P.-T.)
- Department of Biomedicine and Biotechnology, Faculty of Medicine, University of Alcalá, C/19 Av. De Madrid, 28871 Alcalá de Henares, Spain
| | - Marcos Hernando-Gozalo
- Department of Microbiology, Príncipe de Asturias Universitary Hospital, Carretera Alcalá-Meco s/n, 28805 Alcalá de Henares, Spain; (C.R.-C.); (M.H.-G.); (J.C.-G.); (R.P.-T.)
- Department of Organic and Inorganic Chemistry, University of Alcalá, Ctra. Madrid-Barcelona, Km 33, 100, 28805 Alcalá de Henares, Spain
| | - Laura Prieto-Pérez
- Department of Infectious Diseases, IIS-Fundación Jiménez Díaz, Av. De los Reyes Católicos, 2, Moncloa-Aravaca, 28040 Madrid, Spain;
| | - Juan Cuadros-González
- Department of Microbiology, Príncipe de Asturias Universitary Hospital, Carretera Alcalá-Meco s/n, 28805 Alcalá de Henares, Spain; (C.R.-C.); (M.H.-G.); (J.C.-G.); (R.P.-T.)
- Department of Biomedicine and Biotechnology, Faculty of Medicine, University of Alcalá, C/19 Av. De Madrid, 28871 Alcalá de Henares, Spain
| | - Ramón Pérez-Tanoira
- Department of Microbiology, Príncipe de Asturias Universitary Hospital, Carretera Alcalá-Meco s/n, 28805 Alcalá de Henares, Spain; (C.R.-C.); (M.H.-G.); (J.C.-G.); (R.P.-T.)
- Department of Biomedicine and Biotechnology, Faculty of Medicine, University of Alcalá, C/19 Av. De Madrid, 28871 Alcalá de Henares, Spain
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Wang C, Gu Y, Chu Q, Wang X, Ding Y, Qin X, Liu T, Wang S, Liu X, Wang B, Cao H. Gut microbiota and metabolites as predictors of biologics response in inflammatory bowel disease: A comprehensive systematic review. Microbiol Res 2024; 282:127660. [PMID: 38442454 DOI: 10.1016/j.micres.2024.127660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Nonresponse to biologic agents in patients with inflammatory bowel disease (IBD) poses a significant public health burden, and the prediction of response to biologics offers valuable insights for IBD management. Given the pivotal role of gut microbiota and their endogenous metabolites in IBD, we conducted a systematic review to investigate the potential of fecal microbiota and mucosal microbiota and endogenous metabolomic markers as predictors for biotherapy response in IBD patients. A total of 38 studies were included in the review. Following anti-TNF-α treatment, the bacterial community characteristics of IBD patients exhibited a tendency to resemble those observed in healthy controls, indicating an improved clinical response. The levels of endogenous metabolites butyrate and deoxycholic acid were significantly associated with clinical remission following anti-TNF-α therapy. IBD patients who responded well to vedolizumab treatment had higher levels of specific bacteria that produce butyrate, along with increased levels of metabolites such as butyrate, branched-chain amino acids and acetamide following vedolizumab treatment. Crohn's disease patients who responded positively to ustekinumab treatment showed higher levels of Faecalibacterium and lower levels of Escherichia/Shigella. In conclusion, fecal microbiota and mucosal microbiota as well as their endogenous metabolites could provide a predictive tool for assessing the response of IBD patients to various biological agents and serve as a valuable reference for precise drug selection in clinical IBD patients.
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Affiliation(s)
- Chen Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yu Gu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qiao Chu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xin Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yiyun Ding
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiali Qin
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Sinan Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiang Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
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Blake KS, Schwartz DJ, Paruthiyil S, Wang B, Ning J, Isidean SD, Burns DS, Whiteson H, Lalani T, Fraser JA, Connor P, Troth T, Porter CK, Tribble DR, Riddle MS, Gutiérrez RL, Simons MP, Dantas G. Gut microbiome and antibiotic resistance effects during travelers' diarrhea treatment and prevention. mBio 2024; 15:e0279023. [PMID: 38085102 PMCID: PMC10790752 DOI: 10.1128/mbio.02790-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 10/30/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE The travelers' gut microbiome is potentially assaulted by acute and chronic perturbations (e.g., diarrhea, antibiotic use, and different environments). Prior studies of the impact of travel and travelers' diarrhea (TD) on the microbiome have not directly compared antibiotic regimens, and studies of different antibiotic regimens have not considered travelers' microbiomes. This gap is important to be addressed as the use of antibiotics to treat or prevent TD-even in moderate to severe cases or in regions with high infectious disease burden-is controversial based on the concerns for unintended consequences to the gut microbiome and antimicrobial resistance (AMR) emergence. Our study addresses this by evaluating the impact of defined antibiotic regimens (single-dose treatment or daily prophylaxis) on the gut microbiome and resistomes of deployed servicemembers, using samples collected during clinical trials. Our findings indicate that the antibiotic treatment regimens that were studied generally do not lead to adverse effects on the gut microbiome and resistome and identify the relative risks associated with prophylaxis. These results can be used to inform therapeutic guidelines for the prevention and treatment of TD and make progress toward using microbiome information in personalized medical care.
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Affiliation(s)
- Kevin S. Blake
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Drew J. Schwartz
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Women’s Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Srinand Paruthiyil
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jie Ning
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sandra D. Isidean
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
- Naval Medical Research Command, Silver Spring, Maryland, USA
| | - Daniel S. Burns
- Academic Department of Military Medicine, UK Defence Medical Directorate, Birmingham, United Kingdom
| | - Harris Whiteson
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tahaniyat Lalani
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Jamie A. Fraser
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Patrick Connor
- Academic Department of Military Medicine, UK Defence Medical Directorate, Birmingham, United Kingdom
| | - Tom Troth
- Academic Department of Military Medicine, UK Defence Medical Directorate, Birmingham, United Kingdom
| | - Chad K. Porter
- Naval Medical Research Command, Silver Spring, Maryland, USA
| | - David R. Tribble
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Mark S. Riddle
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | | | - Mark P. Simons
- Naval Medical Research Command, Silver Spring, Maryland, USA
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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Campos-Madueno EI, Aldeia C, Perreten V, Sendi P, Moser AI, Endimiani A. Detection of blaCTX-M and blaDHA genes in stool samples of healthy people: comparison of culture- and shotgun metagenomic-based approaches. Front Microbiol 2023; 14:1236208. [PMID: 37720151 PMCID: PMC10501143 DOI: 10.3389/fmicb.2023.1236208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023] Open
Abstract
We implemented culture- and shotgun metagenomic sequencing (SMS)-based methods to assess the gut colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESC-R-Ent) in 42 volunteers. Both methods were performed using native and pre-enriched (broth supplemented with cefuroxime) stools. Native culture screening on CHROMID® ESBL plates resulted in 17 positive samples, whereas the pre-enriched culture (gold-standard) identified 23 carriers. Overall, 26 ESC-R-Ent strains (24 Escherichia coli) were identified: 25 CTX-M and 3 DHA-1 producers (2 co-producing CTX-Ms). Using the SMS on native stool ("native SMS") with thresholds ≥60% for both identity and coverage, only 7 of the 23 pre-enriched culture-positive samples resulted positive for blaCTX-M/blaDHA genes (native SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 59.0%; specificity 100%). Moreover, an average of 31.5 and 24.6 antimicrobial resistance genes (ARGs) were detected in the 23 pre-enriched culture-positive and the 19 negative samples, respectively. When the pre-enriched SMS was implemented, more blaCTX-M/blaDHA genes were detected than in the native assay, including in stools that were pre-enriched culture-negative (pre-enriched SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 78.3%; specificity 75.0%). In addition, the pre-enriched SMS identified on average 38.6 ARGs/sample, whereas for the corresponding native SMS it was 29.4 ARGs/sample. Notably, stools resulting false-negative by using the native SMS had lower concentrations of ESC-R-Ent (average: ~105 vs. ~107 CFU/g) and E. coli classified reads (average: 193,959 vs. 1.45 million) than those of native SMS positive samples. Finally, the detection of blaCTX-M/blaDHA genes was compared with two well-established bioinformatic tools. In conclusion, only the pre-enriched SMS assured detection of most carriers of ESC-R-Ent. However, its performance was not comparable to the pre-enriched culture-based approach.
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Affiliation(s)
- Edgar I. Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Aline I. Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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