Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-producing Enterobacterales carriage: a matched case–control study in infectious diseases department
Little is known about the effect of gut microbial and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) carriage, particularly in the general population. The aim of this study was to identify microbiota signatures uniquely correlated with ESBL-E carriage. We conducted a case–control...
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| Veröffentlicht in: | Clinical microbiology and infection 2024-09, Vol.30 (9), p.1154-1163 |
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| creator | Boyd, Anders El Dani, Mariam Ajrouche, Roula Demontant, Vanessa Cheval, Justine Lacombe, Karine Cosson, Guillaume Rodriguez, Christophe Pawlotsky, Jean-Michel Woerther, Paul-Louis Surgers, Laure |
| description | Little is known about the effect of gut microbial and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) carriage, particularly in the general population. The aim of this study was to identify microbiota signatures uniquely correlated with ESBL-E carriage.
We conducted a case–control study among individuals seeking care at the Sexual Health Clinic or Department of Infectious and Tropical Diseases, Saint-Antoine Hospital, Paris, France. Using coarsened exact matching, 176 participants with ESBL-carriage (i.e. cases) were matched 1:1 to those without ESBL-carriage (i.e. controls) based on sexual group, ESBL-E prevalence of countries travelled in |
| doi_str_mv | 10.1016/j.cmi.2024.03.016 |
| format | Article |
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We conducted a case–control study among individuals seeking care at the Sexual Health Clinic or Department of Infectious and Tropical Diseases, Saint-Antoine Hospital, Paris, France. Using coarsened exact matching, 176 participants with ESBL-carriage (i.e. cases) were matched 1:1 to those without ESBL-carriage (i.e. controls) based on sexual group, ESBL-E prevalence of countries travelled in <12 months, number of sexual partners in <6 months, geographic origin, and any antibiotic use in <6 months. 16S rRNA gene amplicon sequencing was used to generate differential abundances at the genus level and measures of α- and β-diversity.
Participants were mostly men (83.2%, n = 293/352) and had a median age of 33 years (interquartile range: 27–44). Nine genera were found associated with ESBL-E carriage: Proteus (p < 0.0001), Carnobacterium (p < 0.0001), Enterorhabdus (p 0.0079), Catonella (p 0.017), Dermacoccus (p 0.017), Escherichia/Shigella (p 0.021), Kocuria (p 0.023), Bacillus (p 0.040), and Filifactor (p 0.043); however, differences were no longer significant after Benjamini–Hochberg correction (q > 0.05). There were no differences between those with versus without ESBL-E carriage in measures of α-diversity (Shannon Diversity Index, p 0.49; Simpson Diversity Index, p 0.54; and Chao1 Richness Estimator, p 0.16) or β-diversity (Bray–Curtis dissimilarity index, p 0.42).
In this large carefully controlled study, there is lacking evidence that gut microbial composition and diversity is any different between individuals with and without ESBL-E carriage.</description><identifier>ISSN: 1198-743X</identifier><identifier>ISSN: 1469-0691</identifier><identifier>EISSN: 1469-0691</identifier><identifier>DOI: 10.1016/j.cmi.2024.03.016</identifier><identifier>PMID: 38527613</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>16S sequencing ; Adult ; Antibiotic resistance ; beta-Lactamases - genetics ; beta-Lactamases - metabolism ; Carrier State - epidemiology ; Carrier State - microbiology ; Case-Control Studies ; Colonization resistance ; Enterobacteriaceae - classification ; Enterobacteriaceae - drug effects ; Enterobacteriaceae - enzymology ; Enterobacteriaceae - genetics ; Enterobacteriaceae - isolation & purification ; Enterobacteriaceae Infections - epidemiology ; Enterobacteriaceae Infections - microbiology ; ESBL-producing Escherichia coli ; Feces - microbiology ; Female ; France - epidemiology ; Gastrointestinal Microbiome ; Gut microbiome ; Humans ; Life Sciences ; Male ; Middle Aged ; Paris - epidemiology ; RNA, Ribosomal, 16S - genetics</subject><ispartof>Clinical microbiology and infection, 2024-09, Vol.30 (9), p.1154-1163</ispartof><rights>2024 European Society of Clinical Microbiology and Infectious Diseases</rights><rights>Copyright © 2024 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c302t-a9376260967a99ccaae94179f727f417fb01bbc7e1f854f22e85db6c08b9c4553</citedby><cites>FETCH-LOGICAL-c302t-a9376260967a99ccaae94179f727f417fb01bbc7e1f854f22e85db6c08b9c4553</cites><orcidid>0000-0002-6957-9482 ; 0000-0001-9512-8928 ; 0000-0001-8128-4030 ; 0000-0002-9817-5006 ; 0000-0003-0745-7559</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38527613$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.sorbonne-universite.fr/hal-04539691$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Boyd, Anders</creatorcontrib><creatorcontrib>El Dani, Mariam</creatorcontrib><creatorcontrib>Ajrouche, Roula</creatorcontrib><creatorcontrib>Demontant, Vanessa</creatorcontrib><creatorcontrib>Cheval, Justine</creatorcontrib><creatorcontrib>Lacombe, Karine</creatorcontrib><creatorcontrib>Cosson, Guillaume</creatorcontrib><creatorcontrib>Rodriguez, Christophe</creatorcontrib><creatorcontrib>Pawlotsky, Jean-Michel</creatorcontrib><creatorcontrib>Woerther, Paul-Louis</creatorcontrib><creatorcontrib>Surgers, Laure</creatorcontrib><title>Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-producing Enterobacterales carriage: a matched case–control study in infectious diseases department</title><title>Clinical microbiology and infection</title><addtitle>Clin Microbiol Infect</addtitle><description>Little is known about the effect of gut microbial and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) carriage, particularly in the general population. The aim of this study was to identify microbiota signatures uniquely correlated with ESBL-E carriage.
We conducted a case–control study among individuals seeking care at the Sexual Health Clinic or Department of Infectious and Tropical Diseases, Saint-Antoine Hospital, Paris, France. Using coarsened exact matching, 176 participants with ESBL-carriage (i.e. cases) were matched 1:1 to those without ESBL-carriage (i.e. controls) based on sexual group, ESBL-E prevalence of countries travelled in <12 months, number of sexual partners in <6 months, geographic origin, and any antibiotic use in <6 months. 16S rRNA gene amplicon sequencing was used to generate differential abundances at the genus level and measures of α- and β-diversity.
Participants were mostly men (83.2%, n = 293/352) and had a median age of 33 years (interquartile range: 27–44). Nine genera were found associated with ESBL-E carriage: Proteus (p < 0.0001), Carnobacterium (p < 0.0001), Enterorhabdus (p 0.0079), Catonella (p 0.017), Dermacoccus (p 0.017), Escherichia/Shigella (p 0.021), Kocuria (p 0.023), Bacillus (p 0.040), and Filifactor (p 0.043); however, differences were no longer significant after Benjamini–Hochberg correction (q > 0.05). There were no differences between those with versus without ESBL-E carriage in measures of α-diversity (Shannon Diversity Index, p 0.49; Simpson Diversity Index, p 0.54; and Chao1 Richness Estimator, p 0.16) or β-diversity (Bray–Curtis dissimilarity index, p 0.42).
In this large carefully controlled study, there is lacking evidence that gut microbial composition and diversity is any different between individuals with and without ESBL-E carriage.</description><subject>16S sequencing</subject><subject>Adult</subject><subject>Antibiotic resistance</subject><subject>beta-Lactamases - genetics</subject><subject>beta-Lactamases - metabolism</subject><subject>Carrier State - epidemiology</subject><subject>Carrier State - microbiology</subject><subject>Case-Control Studies</subject><subject>Colonization resistance</subject><subject>Enterobacteriaceae - classification</subject><subject>Enterobacteriaceae - drug effects</subject><subject>Enterobacteriaceae - enzymology</subject><subject>Enterobacteriaceae - genetics</subject><subject>Enterobacteriaceae - isolation & purification</subject><subject>Enterobacteriaceae Infections - epidemiology</subject><subject>Enterobacteriaceae Infections - microbiology</subject><subject>ESBL-producing Escherichia coli</subject><subject>Feces - microbiology</subject><subject>Female</subject><subject>France - epidemiology</subject><subject>Gastrointestinal Microbiome</subject><subject>Gut microbiome</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Male</subject><subject>Middle Aged</subject><subject>Paris - epidemiology</subject><subject>RNA, Ribosomal, 16S - genetics</subject><issn>1198-743X</issn><issn>1469-0691</issn><issn>1469-0691</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9UU1u1TAQjhCIlsIB2CAvYZFgx_kzrKqqtEhPYgMSO8uxJ31-iuOH7bzydtyBm3APOAQnYUJKl0iW_Hnmm2_G82XZc0YLRlnzeldoZ4uSllVBeYGRB9kpqxqR00awh4iZ6PK24p9Psicx7iilJefV4-yEd3XZNoyfZj-v5kSc1cH31jsgxh4gRJuORE2GaO_2Hl_WT8QuB9PWzGqM5Nam7V_OAjyKwNcEkwGTxz3oFGZHfv3IR6WTcipCvg_ezNpON-RySoDtMANBjRCJViFYdQNviCJOJb0F7Iw1v799135KwY8kptkc1xEGVLd-jjhqBGQhgL0KycGUnmaPBhwOnt3dZ9mnd5cfL67zzYer9xfnm1xzWqZcCd42ZUNF0yohtFYKRMVaMbRlOyAYesr6XrfAhq6uhrKErjZ9o2nXC13VNT_LXq26WzXKfbBOhaP0ysrr841cYrSquUATDgy5L1cubuDLDDFJZ6OGcVQT4DckpxWnbcNph1S2UtGOGAMM99qMysVxuZPouFwcl5RLjGDNizv5uXdg7iv-WYyEtysBcCEHC0FGbWHSYGzAVUrj7X_k_wDgzsOG</recordid><startdate>20240901</startdate><enddate>20240901</enddate><creator>Boyd, Anders</creator><creator>El Dani, Mariam</creator><creator>Ajrouche, Roula</creator><creator>Demontant, Vanessa</creator><creator>Cheval, Justine</creator><creator>Lacombe, Karine</creator><creator>Cosson, Guillaume</creator><creator>Rodriguez, Christophe</creator><creator>Pawlotsky, Jean-Michel</creator><creator>Woerther, Paul-Louis</creator><creator>Surgers, Laure</creator><general>Elsevier Ltd</general><general>Elsevier for the European Society of Clinical Microbiology and Infectious Diseases</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>1XC</scope><scope>VOOES</scope><orcidid>https://orcid.org/0000-0002-6957-9482</orcidid><orcidid>https://orcid.org/0000-0001-9512-8928</orcidid><orcidid>https://orcid.org/0000-0001-8128-4030</orcidid><orcidid>https://orcid.org/0000-0002-9817-5006</orcidid><orcidid>https://orcid.org/0000-0003-0745-7559</orcidid></search><sort><creationdate>20240901</creationdate><title>Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-producing Enterobacterales carriage: a matched case–control study in infectious diseases department</title><author>Boyd, Anders ; El Dani, Mariam ; Ajrouche, Roula ; Demontant, Vanessa ; Cheval, Justine ; Lacombe, Karine ; Cosson, Guillaume ; Rodriguez, Christophe ; Pawlotsky, Jean-Michel ; Woerther, Paul-Louis ; Surgers, Laure</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c302t-a9376260967a99ccaae94179f727f417fb01bbc7e1f854f22e85db6c08b9c4553</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>16S sequencing</topic><topic>Adult</topic><topic>Antibiotic resistance</topic><topic>beta-Lactamases - genetics</topic><topic>beta-Lactamases - metabolism</topic><topic>Carrier State - epidemiology</topic><topic>Carrier State - microbiology</topic><topic>Case-Control Studies</topic><topic>Colonization resistance</topic><topic>Enterobacteriaceae - classification</topic><topic>Enterobacteriaceae - drug effects</topic><topic>Enterobacteriaceae - enzymology</topic><topic>Enterobacteriaceae - genetics</topic><topic>Enterobacteriaceae - isolation & purification</topic><topic>Enterobacteriaceae Infections - epidemiology</topic><topic>Enterobacteriaceae Infections - microbiology</topic><topic>ESBL-producing Escherichia coli</topic><topic>Feces - microbiology</topic><topic>Female</topic><topic>France - epidemiology</topic><topic>Gastrointestinal Microbiome</topic><topic>Gut microbiome</topic><topic>Humans</topic><topic>Life Sciences</topic><topic>Male</topic><topic>Middle Aged</topic><topic>Paris - epidemiology</topic><topic>RNA, Ribosomal, 16S - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Boyd, Anders</creatorcontrib><creatorcontrib>El Dani, Mariam</creatorcontrib><creatorcontrib>Ajrouche, Roula</creatorcontrib><creatorcontrib>Demontant, Vanessa</creatorcontrib><creatorcontrib>Cheval, Justine</creatorcontrib><creatorcontrib>Lacombe, Karine</creatorcontrib><creatorcontrib>Cosson, Guillaume</creatorcontrib><creatorcontrib>Rodriguez, Christophe</creatorcontrib><creatorcontrib>Pawlotsky, Jean-Michel</creatorcontrib><creatorcontrib>Woerther, Paul-Louis</creatorcontrib><creatorcontrib>Surgers, Laure</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><jtitle>Clinical microbiology and infection</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Boyd, Anders</au><au>El Dani, Mariam</au><au>Ajrouche, Roula</au><au>Demontant, Vanessa</au><au>Cheval, Justine</au><au>Lacombe, Karine</au><au>Cosson, Guillaume</au><au>Rodriguez, Christophe</au><au>Pawlotsky, Jean-Michel</au><au>Woerther, Paul-Louis</au><au>Surgers, Laure</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-producing Enterobacterales carriage: a matched case–control study in infectious diseases department</atitle><jtitle>Clinical microbiology and infection</jtitle><addtitle>Clin Microbiol Infect</addtitle><date>2024-09-01</date><risdate>2024</risdate><volume>30</volume><issue>9</issue><spage>1154</spage><epage>1163</epage><pages>1154-1163</pages><issn>1198-743X</issn><issn>1469-0691</issn><eissn>1469-0691</eissn><abstract>Little is known about the effect of gut microbial and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) carriage, particularly in the general population. The aim of this study was to identify microbiota signatures uniquely correlated with ESBL-E carriage.
We conducted a case–control study among individuals seeking care at the Sexual Health Clinic or Department of Infectious and Tropical Diseases, Saint-Antoine Hospital, Paris, France. Using coarsened exact matching, 176 participants with ESBL-carriage (i.e. cases) were matched 1:1 to those without ESBL-carriage (i.e. controls) based on sexual group, ESBL-E prevalence of countries travelled in <12 months, number of sexual partners in <6 months, geographic origin, and any antibiotic use in <6 months. 16S rRNA gene amplicon sequencing was used to generate differential abundances at the genus level and measures of α- and β-diversity.
Participants were mostly men (83.2%, n = 293/352) and had a median age of 33 years (interquartile range: 27–44). Nine genera were found associated with ESBL-E carriage: Proteus (p < 0.0001), Carnobacterium (p < 0.0001), Enterorhabdus (p 0.0079), Catonella (p 0.017), Dermacoccus (p 0.017), Escherichia/Shigella (p 0.021), Kocuria (p 0.023), Bacillus (p 0.040), and Filifactor (p 0.043); however, differences were no longer significant after Benjamini–Hochberg correction (q > 0.05). There were no differences between those with versus without ESBL-E carriage in measures of α-diversity (Shannon Diversity Index, p 0.49; Simpson Diversity Index, p 0.54; and Chao1 Richness Estimator, p 0.16) or β-diversity (Bray–Curtis dissimilarity index, p 0.42).
In this large carefully controlled study, there is lacking evidence that gut microbial composition and diversity is any different between individuals with and without ESBL-E carriage.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>38527613</pmid><doi>10.1016/j.cmi.2024.03.016</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0002-6957-9482</orcidid><orcidid>https://orcid.org/0000-0001-9512-8928</orcidid><orcidid>https://orcid.org/0000-0001-8128-4030</orcidid><orcidid>https://orcid.org/0000-0002-9817-5006</orcidid><orcidid>https://orcid.org/0000-0003-0745-7559</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Clinical microbiology and infection, 2024-09, Vol.30 (9), p.1154-1163 |
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| subjects | 16S sequencing Adult Antibiotic resistance beta-Lactamases - genetics beta-Lactamases - metabolism Carrier State - epidemiology Carrier State - microbiology Case-Control Studies Colonization resistance Enterobacteriaceae - classification Enterobacteriaceae - drug effects Enterobacteriaceae - enzymology Enterobacteriaceae - genetics Enterobacteriaceae - isolation & purification Enterobacteriaceae Infections - epidemiology Enterobacteriaceae Infections - microbiology ESBL-producing Escherichia coli Feces - microbiology Female France - epidemiology Gastrointestinal Microbiome Gut microbiome Humans Life Sciences Male Middle Aged Paris - epidemiology RNA, Ribosomal, 16S - genetics |
| title | Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-producing Enterobacterales carriage: a matched case–control study in infectious diseases department |
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