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Park DE, Aziz M, Koch BJ, Roach K, Clabots C, Johnson JR, Price LB, Liu CM. Gut microbiome predictors of Escherichia coli sequence type 131 colonization and loss. EBioMedicine 2024; 99:104909. [PMID: 38096689 PMCID: PMC10758731 DOI: 10.1016/j.ebiom.2023.104909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 11/15/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Escherichia coli sequence type 131 (ST131), specifically its fluoroquinolone-resistant H30R clade (ST131-H30R), is a global multidrug-resistant pathogen. The gut microbiome's role in ST131-H30R intestinal carriage is undefined. METHODS Veterans and their household members underwent longitudinal fecal swab surveillance for ST131 in 2014-2018. The fecal microbiome was characterized by 16S rRNA qPCR and sequencing. We evaluated associations between ST131-H30R carriage and gut microbiome at baseline by random forest models to identify the most informative gut bacterial phyla and genera attributes for ST131 and ST131-H30R carriage status. Next, we assessed longitudinal associations between fecal microbiome and ST131-H30R carriage using a mixed-effects logistic regression with longitudinal measures. FINDINGS Of the 519 participants, 78 were carriers of ST131, among whom 49 had ST131-H30R. At the baseline timepoint, H30R-positive participants had higher proportional abundances of Actinobacteria phylum (mean: 4.9% vs. 3.1%) than ST131-negative participants. H30R-positive participants also had higher abundances of Collinsella (mean: 2.3% vs. 1.1%) and lower abundances of Alistipes (mean: 2.1% vs. 2.6%) than ST131-negative participants. In the longitudinal analysis, Collinsella abundance correlated positively with ST131-H30R carriage status and negatively with the loss of ST131-H30R. Conversely, Alistipes corresponded with the loss and persistent absence of ST131-H30R even in the presence of a household exposure. INTERPRETATION Abundances of specific fecal bacteria correlated with ST131-H30R carriage, persistence, and loss, suggesting their potential as targets for microbiome-based strategies to reduce carriage of ST131-H30R, a significant risk factor for invasive infections. FUNDING This work was supported in part by National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award numbers R21AI117654 and UM1AI104681 and the Office of Research and Development, Department of Veterans Affairs. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the Department of Veterans Affairs.
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Affiliation(s)
- Daniel E Park
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Maliha Aziz
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, P.O. Box 5620, Flagstaff, AZ, 86011, USA; Department of Biological Sciences, Northern Arizona University, 617 S Beaver St., Flagstaff, AZ, 86011, USA
| | - Kelsey Roach
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Connie Clabots
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN, 55417, USA
| | - James R Johnson
- Minneapolis Veterans Affairs Health Care System, 1 Veterans Dr, Minneapolis, MN, 55417, USA; Department of Medicine, University of Minnesota, 401 East River Parkway, VCRC 1st, UK Floor, Suite 131, Minneapolis, MN, 55455, USA
| | - Lance B Price
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Cindy M Liu
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA.
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Resistência microbiana a medicamentos em uma Instituição de Longa Permanência para Idosos. ACTA PAUL ENFERM 2022. [DOI: 10.37689/acta-ape/2022ao03751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Larcombe S, Hutton ML, Lyras D. Hyperimmune bovine colostrum reduces gastrointestinal carriage of uropathogenic Escherichia coli. Hum Vaccin Immunother 2018; 15:508-513. [PMID: 30277834 DOI: 10.1080/21645515.2018.1528836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Debilitating recurrent urinary tract infections (UTIs) are often associated with gastrointestinal colonisation by uropathogens, such as uropathogenic Escherichia coli (UPEC), suggesting that these populations might be a suitable target for the treatment and prevention of recurrent UTI. However, antimicrobial treatment is generally unable to prevent recurrent UTI, and often selects for multidrug resistant uropathogens in the gut, and causes dysbiosis of the gut, vaginal, and urinary microbiota. Of note, the globally-disseminated multi drug resistant UPEC lineage, ST131, is known to both persistently colonise the gut and the urinary tract, and is associated with antibiotic treatment failure, indicating the need for novel non-antibiotic therapeutics for the treatment of UTI. This study therefore presents hyperimmune bovine colostrum (HBC) as a suitable therapy for the treatment of UPEC gastrointestinal colonisation. This work demonstrates that the vaccination of pregnant cows with inactivated cells from a ST131 UPEC isolate results in a highly specific anti-UPEC HBC, and that this product is able to disrupt the gastrointestinal colonisation of ST131 UPEC in mice.
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Affiliation(s)
- Sarah Larcombe
- a Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton , VIC , Australia
| | - Melanie L Hutton
- a Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton , VIC , Australia
| | - Dena Lyras
- a Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton , VIC , Australia
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Nicolas-Chanoine MH, Petitjean M, Mora A, Mayer N, Lavigne JP, Boulet O, Leflon-Guibout V, Blanco J, Hocquet D. The ST131 Escherichia coli H22 subclone from human intestinal microbiota: Comparison of genomic and phenotypic traits with those of the globally successful H30 subclone. BMC Microbiol 2017; 17:71. [PMID: 28347271 PMCID: PMC5369007 DOI: 10.1186/s12866-017-0984-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 03/14/2017] [Indexed: 01/11/2023] Open
Abstract
Background In 2006, we found healthy subjects carrying ST131 Escherichia coli in their intestinal microbiota consisting of two populations: a subdominant population of fluoroquinolone-resistant E. coli belonging to subclone H30 (H30-R or subclade C1), the current worldwide dominant ST131 subclone, and a dominant E. coli population composed of antibiotic-susceptible E. coli belonging to subclone H22 (clade B), the precursor of subclone H30. We sequenced the whole genome of fecal H22 strain S250, compared it to the genomes of ExPEC ST131 H30-Rx strain JJ1886 and commensal ST131 H41 strain SE15, sought the H22-H30 genomic differences in our fecal strains and assessed their phenotypic consequences. Results We detected 173 genes found in the Virulence Factor Database, of which 148 were shared by the three ST131 genomes, whereas some were genome-specific, notably those allowing determination of virotype (D for S250 and C for JJ1886). We found three sequences of the FimH site involved in adhesion: two in S250 and SE15 close and identical, respectively, to that previously reported to confer strong intestinal adhesion, and one in JJ1886, corresponding to that commonly present in uropathogenic E. coli. Among the genes involved in sugar metabolism, one encoding a gluconate kinase lacked in S250 and JJ1886. Although this gene was also absent in both our fecal H22 and H30-R strains, H22 strains showed a higher capacity to grow in minimal medium with gluconate. Among the genes involved in gluconate metabolism, only the ghrB gene differed between S250/H22 and JJ1886/H30-R strains, resulting in different gluconate reductases. Of the genes involved in biofilm formation, two were absent in the three genomes and one, fimB, in the JJ1886 genome. Our fecal H30-R strains lacking intact fimB displayed delayed biofilm formation relative to our fecal H22 strains. The H22 strains differed by subclade B type and plasmid content, whereas the H30-R strains were identical. Conclusions Phenotypic analysis of our fecal strains based on observed genomic differences between S250 and JJ1886 strains suggests the presence of traits related to bacterial commensalism in our H22 strains and traits commonly found in uropathogenic E. coli in our H30-R strains. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0984-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie-Hélène Nicolas-Chanoine
- Service de Microbiologie, Hôpital Beaujon, AP-HP, Clichy, France. .,Faculté de Médecine Paris Diderot, Paris, France. .,INSERM UMR 1137, Université Paris 7, Paris, France.
| | - Marie Petitjean
- Laboratoire d'Hygiène Hospitalière, CHRU Besançon, Besançon, France.,UMR 6249 Chrono-Environnement, Besançon, France
| | - Azucena Mora
- Laboratorio de Referencia de E. coli (LREC), Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Noémie Mayer
- Service de Microbiologie, Hôpital Beaujon, AP-HP, Clichy, France
| | - Jean-Philippe Lavigne
- Institut National de la Santé et de la Recherche Médicale, U1047, Université de Montpellier, UFR de Médecine, Nîmes, France.,Service de Microbiologie, CHU Carémeau, Nîmes, France
| | - Olivier Boulet
- Laboratoire d'Analyse Médicale du Centre, Coulommiers, France
| | | | - Jorge Blanco
- Laboratorio de Referencia de E. coli (LREC), Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Didier Hocquet
- Laboratoire d'Hygiène Hospitalière, CHRU Besançon, Besançon, France.,UMR 6249 Chrono-Environnement, Besançon, France
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Livorsi DJ, Goto M, Carrel M, Jones MM, McDanel J, Nair R, Alexander B, Beck B, Richardson KK, Perencevich EN. Regional variations in fluoroquinolone non-susceptibility among Escherichia coli bloodstream infections within the Veterans Healthcare Administration. Antimicrob Resist Infect Control 2016; 5:38. [PMID: 27777759 PMCID: PMC5069952 DOI: 10.1186/s13756-016-0135-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/27/2016] [Indexed: 12/03/2022] Open
Abstract
Objectives We sought to define regional variations in fluoroquinolone non-susceptibility (FQ-NS) among bloodstream isolates of Escherichia coli across the Veterans Health Administration (VHA) in the United States. Methods We analyzed a retrospective cohort of patients managed at 136 VHA hospitals who had a blood culture positive for E.coli between 2003 and 2013. Hospitals were classified based on US Census Divisions, and regional variations in FQ-NS were analyzed. Results Twenty-four thousand five hundred twenty-three unique E.coli bloodstream infections (BSIs) were identified between 2003 and 2013. 53.9 % of these were community-acquired, 30.7 % were healthcare-associated, and 15.4 % were hospital-onset BSIs. The proportion of E.coli BSIs with FQ-NS significantly varied across US Census Divisions (p < 0.001). During 2003–2013, the proportion of E.coli BSIs with FQ-NS was highest in the West South-Central Division (32.7 %) and lowest in the Mountain Division (20.0 %). Multivariable analysis showed that there were universal secular trends towards higher FQ-NS rates (p < 0.001) with significant variability of slopes across US Census Divisions (p < 0.001). Conclusion There has been a universal increase in FQ-NS among E.coli BSIs within VHA, but the rate of increase has significantly varied across Census Divisions. The reasons for this variability are unclear. These findings reinforce the importance of using local data to develop and update local antibiograms and antibiotic-prescribing guidelines.
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Affiliation(s)
- Daniel J Livorsi
- Iowa City VA Health Care System, Iowa City, IA USA ; Division of Infectious Diseases, Department of Internal Medicine, University of Iowa Carver College of Medicine, 200 Hawkins Drive, Iowa City, IA 52242 USA
| | - Michihiko Goto
- Iowa City VA Health Care System, Iowa City, IA USA ; Division of Infectious Diseases, Department of Internal Medicine, University of Iowa Carver College of Medicine, 200 Hawkins Drive, Iowa City, IA 52242 USA
| | - Margaret Carrel
- Department of Geographical and Sustainability Sciences, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA USA
| | - Makoto M Jones
- Salt Lake City VA Health Care System, Salt Lake City, UT USA ; University of Utah School of Medicine, Salt Lake City, UT USA
| | - Jennifer McDanel
- Iowa City VA Health Care System, Iowa City, IA USA ; Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA USA
| | - Rajeshwari Nair
- Iowa City VA Health Care System, Iowa City, IA USA ; Division of General Internal Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA USA
| | | | - Brice Beck
- Iowa City VA Health Care System, Iowa City, IA USA
| | | | - Eli N Perencevich
- Iowa City VA Health Care System, Iowa City, IA USA ; Division of General Internal Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA USA
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