Gut microbiome perturbation, antibiotic resistance, and Escherichia coli strain dynamics associated with international travel: a metagenomic analysis.

Autor:	Worby CJ; Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA., Sridhar S; Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA., Turbett SE; Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA., Becker MV; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA., Kogut L; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA., Sanchez V; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA., Bronson RA; Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA., Rao SR; Department of Global Health, Boston University School of Public Health, Boston, MA, USA., Oliver E; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA., Walker AT; Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, GA, USA., Walters MS; Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA, USA., Kelly P; Division of Infectious Diseases, Bronx Care Center, Bronx, NY, USA., Leung DT; Division of Infectious Diseases and Division of Microbiology and Immunology, University of Utah, Salt Lake City, UT, USA., Knouse MC; Department of Medicine, Lehigh Valley Health Network, Allentown, PA, USA., Hagmann SHF; Division of Pediatric Infectious Diseases, Steven and Alexandra Cohen Children's Medical Center of New York/Northwell Health, New Hyde Park, NY, USA., Harris JB; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Division of Pediatric Global Health, Massachusetts General Hospital for Children, Boston, MA, USA., Ryan ET; Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Travellers' Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA., Earl AM; Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: aearl@broadinstitute.org., LaRocque RC; Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA; Travellers' Advice and Immunization Center, Massachusetts General Hospital, Boston, MA, USA.
Jazyk:	angličtina
Zdroj:	The Lancet. Microbe [Lancet Microbe] 2023 Oct; Vol. 4 (10), pp. e790-e799. Date of Electronic Publication: 2023 Sep 13.
DOI:	10.1016/S2666-5247(23)00147-7
Abstrakt:	Background: Culture-based studies have shown that acquisition of extended-spectrum β-lactamase-producing Enterobacterales is common during international travel; however, little is known about the role of the gut microbiome before and during travel, nor about acquisition of other antimicrobial-resistant organisms. We aimed to identify (1) whether the gut microbiome provided colonisation resistance against antimicrobial-resistant organism acquisition, (2) the effect of travel and travel behaviours on the gut microbiome, and (3) the scale and global heterogeneity of antimicrobial-resistant organism acquisition. Methods: In this metagenomic analysis, participants were recruited at three US travel clinics (Boston, MA; New York, NY; and Salt Lake City, UT) before international travel. Participants had to travel internationally between Dec 8, 2017, and April 30, 2019, and have DNA extractions for stool samples both before and after travel for inclusion. Participants were excluded if they had at least one low coverage sample (<1 million read pairs). Stool samples were collected at home before and after travel, sent to a clinical microbiology laboratory to be screened for three target antimicrobial-resistant organisms (extended-spectrum β-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales, and mcr-mediated colistin-resistant Enterobacterales), and underwent DNA extraction and shotgun metagenomic sequencing. We profiled metagenomes for taxonomic composition, antibiotic-resistant gene content, and characterised the Escherichia coli population at the strain level. We analysed pre-travel samples to identify the gut microbiome risk factors associated with acquisition of the three targeted antimicrobial resistant organisms. Pre-travel and post-travel samples were compared to identify microbiome and resistome perturbation and E coli strain acquisition associated with travel. Findings: A total of 368 individuals travelled between the required dates, and 296 had DNA extractions available for both before and after travel. 29 travellers were excluded as they had at least one low coverage sample, leaving a final group of 267 participants. We observed a perturbation of the gut microbiota, characterised by a significant depletion of microbial diversity and enrichment of the Enterobacteriaceae family. Metagenomic strain tracking confirmed that 67% of travellers acquired new strains of E coli during travel that were phylogenetically distinct from their pre-travel strains. We observed widespread enrichment of antibiotic-resistant genes in the gut, with a median 15% (95% CI 10-20, p<1 × 10 -10 ) increase in burden (reads per kilobase per million reads). This increase included antibiotic-resistant genes previously classified as threats to public health, which were 56% (95% CI 36-91, p=2 × 10 -11 ) higher in abundance after travel than before. Fluoroquinolone antibiotic-resistant genes were aquired by 97 (54%) of 181 travellers with no detected pre-travel carriage. Although we found that visiting friends or relatives, travel to south Asia, and eating uncooked vegetables were risk factors for acquisition of the three targeted antimicrobial resistant organisms, we did not observe an association between the pre-travel microbiome structure and travel-related antimicrobial-resistant organism acquisition. Interpretation: This work highlights a scale of E coli and antimicrobial-resistant organism acquisition by US travellers not apparent from previous culture-based studies, and suggests that strategies to control antimicrobial-resistant organisms addressing international traveller behaviour, rather than modulating the gut microbiome, could be worthwhile. Funding: US Centers for Disease Control and Prevention and National Institute of Allergy and Infectious Diseases. Competing Interests: Declaration of interests SET is a Committee Member for the American Society of Transplantation Consensus Conference on Novel Infectious Disease Diagnostics in Solid Organ Transplant, Subgroup Leader on the Rapid Antimicrobial Resistance Detection Methods Subgroup, and received funding within the past 36 months from the Massachusetts General Hospital Vickery-Colvin Grant. DTL is a councillor on Clinical Group, Member of the Scientific Program Committee for American Society of Tropical Medicine and Hygiene, and received authorship royalties from UpToDate. JBH provided editorial services for UpToDate. RCL received payments for editorial services from UpToDate and the US Centers for Disease Control and Prevention Foundation. All other authors declare no competing interests. (Copyright © 2023 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)
Databáze:	MEDLINE
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