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Litchman E, Villéger S, Zinger L, Auguet JC, Thuiller W, Munoz F, Kraft NJB, Philippot L, Violle C. Refocusing the microbial rare biosphere concept through a functional lens. Trends Ecol Evol 2024; 39:923-936. [PMID: 38987022 DOI: 10.1016/j.tree.2024.06.005] [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: 10/06/2023] [Revised: 06/04/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024]
Abstract
The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions.
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Affiliation(s)
- Elena Litchman
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA; Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA.
| | | | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300, CNRS, Institut de Recherche pour le Développement (IRD), Toulouse INP, Université Toulouse 3 Paul Sabatier, Toulouse, France
| | | | - Wilfried Thuiller
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - François Munoz
- Université Grenoble Alpes, CNRS, LIPhy, F-38000 Grenoble, France
| | - Nathan J B Kraft
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRAE, Institut Agro Dijon, Agroecology, Dijon, France
| | - Cyrille Violle
- CEFE, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
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Tchesnokova V, Larson L, Basova I, Sledneva Y, Choudhury D, Solyanik T, Heng J, Bonilla TC, Pasumansky I, Bowers V, Pham S, Madziwa LT, Holden E, Tartof SY, Ralston JD, Sokurenko EV. Gut resident Escherichia coli profile predicts the eighteen-month probability and antimicrobial susceptibility of urinary tract infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24305377. [PMID: 38645148 PMCID: PMC11030298 DOI: 10.1101/2024.04.05.24305377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Community-acquired UTI is the most common bacterial infection managed in general medical practice that can lead to life-threatening outcomes. While UTIs are primarily caused by Escherichia coli colonizing the patient's gut, it is unclear whether the gut resident E. coli profiles can predict the person's risks for UTI and optimal antimicrobial treatments. Thus, we conducted an eighteen-month long community-based observational study of fecal E. coli colonization and UTI in women aged 50 years and above. Methods and Findings We enrolled a total of 1,804 women distributed among age groups 50-59 yo (437 participants), 60-69 yo (632), 70-79 yo (532), and above 80 yo (203), lacking antibiotic prescriptions for at least one year. The provided fecal samples were plated for the presence of E. coli and other enterobacteria resistant to trimethoprim/sulfamethoxazole (TMP/STX), ciprofloxacin (CIP) and 3rd generation cephalosporins (3GC). E. coli was also characterized as belonging to the pandemic multi-drug resistant clonal groups ST131 (subclone H30) and ST1193. Following sample collection, the women were monitored for 18 months for occurrence of UTI.E. coli was cultured from 90.8% fecal samples, with 24.1% containing bacteria resistant to TMP/STX, 19.4% to CIP, and 7.9% to 3GC. In 62.5% samples, only all-susceptible E. coli were present. Overall, there were no age-related differences in resistance prevalence. However, while the total E. coli H30 and ST1193 carriage rates were similar (4.3% and 4.2%, respectively), there was a notable increase of H30 carriage with age (P = .001), while carriage decreased with age for ST1193 (P = .057).Within 18 months, 184 women (10.2%) experienced at least one episode of UTI - 10.9% among the gut E. coli carriers and 3.0% among the non-carriers (P=.0013). The UTI risk among carriers of E. coli H30 but not ST1193 was significantly above average (24.3%, P = .0004). The UTI probability increased with age, occurring in 6.4% of 50-59 yo and 19.7% of 80+ yo (P<.001), with the latter group being especially at high risk for UTI, if they were colonized by E. coli H30 (40.0%, P<.001).E. coli was identified in 88.1% of urine samples, with 16.1% resistant to TMP/STX, 16.1% to CIP, 4.2% to 3GC and 73.1% to none of the antibiotics. Among tested urinary E. coli resistant to antibiotics, 86.1% matched the resistance profile of E. coli in the fecal samples, with the clonotyping and whole genome sequencing confirming the matching strains' identity. Positive predictive value (PPV) of using gut resistance profiles to predict UTI pathogens' susceptibility to TMP/STX, CIP, 3GC and all three antibiotics were 98.4%, 98.3%, 96.6% and 95.3%, respectively. Corresponding negative predictive values (NPV) were 63.0%, 54.8%, 44.4% and 75.8%, respectively. The AUC ROC curve values for the accuracy of fecal diagnostic testing for the prediction of UTI resistance ranged .86-.89. The fecal test-guided drug-bug mismatch rate for empirical (pre-culture) prescription of TMP-SXT or CIP is reduced to ≤2% in 89.6% of patients and 94.8% of patients with an optional 3GC prescription. Conclusion The resistance profile and clonal identity of gut colonizing E. coli, along with the carrier's age, can inform personalized prediction of a patients' UTI risk and the UTI pathogen's antibiotic susceptibility within an 18-month period.
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Affiliation(s)
- Veronika Tchesnokova
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Lydia Larson
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Irina Basova
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Yulia Sledneva
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Debarati Choudhury
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Thalia Solyanik
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Jennifer Heng
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Teresa Cristina Bonilla
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Isaac Pasumansky
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Victoria Bowers
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Sophia Pham
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Lawrence T. Madziwa
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA 98101-1466, USA
| | - Erika Holden
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA 98101-1466, USA
| | - Sara Y. Tartof
- Kaiser Permanente Southern California, Department of Research & Evaluation, Pasadena, 100 S Los Robles, Pasadena, CA 91101, USA
- Kaiser Permanente Bernard J. Tyson School of Medicine, Department of Health Systems Science, 100 S Los Robles, Pasadena, CA 91101, USA
| | - James D. Ralston
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA 98101-1466, USA
| | - Evgeni V. Sokurenko
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA
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Hawas S, Vagenas D, Haque A, Totsika M. Bladder-draining lymph nodes support germinal center B cell responses during urinary tract infection in mice. Infect Immun 2023; 91:e0031723. [PMID: 37882531 PMCID: PMC10652902 DOI: 10.1128/iai.00317-23] [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: 08/12/2023] [Accepted: 10/02/2023] [Indexed: 10/27/2023] Open
Abstract
Bacterial urinary tract infections (UTIs) are both common and exhibit high recurrence rates in women. UTI healthcare costs are increasing due to the rise of multidrug-resistant (MDR) bacteria, necessitating alternative approaches for infection control. Here, we directly observed host adaptive immune responses in acute UTI. We employed a mouse model in which wild-type C57BL/6J mice were transurethrally inoculated with a clinically relevant MDR UTI strain of uropathogenic Escherichia coli (UPEC). Firstly, we noted that rag1-/- C57BL/6J mice harbored larger bacterial burdens than wild-type counterparts, consistent with a role for adaptive immunity in UTI control. Consistent with this, UTI triggered in the bladders of wild-type mice early increases of myeloid cells, including CD11chi conventional dendritic cells, suggesting possible involvement of these professional antigen-presenting cells. Importantly, germinal center B cell responses developed by 4 weeks post-infection in bladder-draining lymph nodes of wild-type mice and, although modest in magnitude and transient in nature, could not be boosted with a second UTI. Thus, our data reveal for the first time in a mouse model that UPEC UTI induces local B cell immune responses in bladder-draining lymph nodes, which could potentially serve to control infection.
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Affiliation(s)
- Sophia Hawas
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Dimitrios Vagenas
- Research Methods Group, School of Public Health and Social Work, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Ashraful Haque
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
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Balbuena-Alonso MG, Camps M, Cortés-Cortés G, Carreón-León EA, Lozano-Zarain P, Rocha-Gracia RDC. Strain belonging to an emerging, virulent sublineage of ST131 Escherichia coli isolated in fresh spinach, suggesting that ST131 may be transmissible through agricultural products. Front Cell Infect Microbiol 2023; 13:1237725. [PMID: 37876872 PMCID: PMC10591226 DOI: 10.3389/fcimb.2023.1237725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/15/2023] [Indexed: 10/26/2023] Open
Abstract
Food contamination with pathogenic Escherichia coli can cause severe disease. Here, we report the isolation of a multidrug resistant strain (A23EC) from fresh spinach. A23EC belongs to subclade C2 of ST131, a virulent clone of Extraintestinal Pathogenic E. coli (ExPEC). Most A23EC virulence factors are concentrated in three pathogenicity islands. These include PapGII, a fimbrial tip adhesin linked to increased virulence, and CsgA and CsgB, two adhesins known to facilitate spinach leaf colonization. A23EC also bears TnMB1860, a chromosomally-integrated transposon with the demonstrated potential to facilitate the evolution of carbapenem resistance among non-carbapenemase-producing enterobacterales. This transposon consists of two IS26-bound modular translocatable units (TUs). The first TU carries aac(6')-lb-cr, bla OXA-1, ΔcatB3, aac(3)-lle, and tmrB, and the second one harbors bla CXT-M-15. A23EC also bears a self-transmissible plasmid that can mediate conjugation at 20°C and that has a mosaic IncF [F(31,36):A(4,20):B1] and Col156 origin of replication. Comparing A23EC to 86 additional complete ST131 sequences, A23EC forms a monophyletic cluster with 17 other strains that share the following four genomic traits: (1) virotype E (papGII+); (2) presence of a PAI II536-like pathogenicity island with an additional cnf1 gene; (3) presence of chromosomal TnMB1860; and (4) frequent presence of an F(31,36):A(4,20):B1 plasmid. Sequences belonging to this cluster (which we named "C2b sublineage") are highly enriched in septicemia samples and their associated genetic markers align with recent reports of an emerging, virulent sublineage of the C2 subclade, suggesting significant pathogenic potential. This is the first report of a ST131 strain belonging to subclade C2 contaminating green leafy vegetables. The detection of this uropathogenic clone in fresh food is alarming. This work suggests that ST131 continues to evolve, gaining selective advantages and new routes of transmission. This highlights the pressing need for rigorous epidemiological surveillance of ExPEC in vegetables with One Health perspective.
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Affiliation(s)
- Maria G. Balbuena-Alonso
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Manel Camps
- Departament of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, United States
| | - Gerardo Cortés-Cortés
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
- Departament of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, United States
| | - Eder A. Carreón-León
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Chihuahua, Mexico
| | - Patricia Lozano-Zarain
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Rosa del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
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Connor CH, Zucoloto AZ, Munnoch JT, Yu IL, Corander J, Hoskisson PA, McDonald B, McNally A. Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract. PLoS Biol 2023; 21:e3002329. [PMID: 37847672 PMCID: PMC10581457 DOI: 10.1371/journal.pbio.3002329] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) can cause a variety of infections outside of the intestine and are a major causative agent of urinary tract infections. Treatment of these infections is increasingly frustrated by antimicrobial resistance (AMR) diminishing the number of effective therapies available to clinicians. Incidence of multidrug resistance (MDR) is not uniform across the phylogenetic spectrum of E. coli. Instead, AMR is concentrated in select lineages, such as ST131, which are MDR pandemic clones that have spread AMR globally. Using a gnotobiotic mouse model, we demonstrate that an MDR E. coli ST131 is capable of out-competing and displacing non-MDR E. coli from the gut in vivo. This is achieved in the absence of antibiotic treatment mediating a selective advantage. In mice colonised with non-MDR E. coli strains, challenge with MDR E. coli either by oral gavage or co-housing with MDR E. coli colonised mice results in displacement and dominant intestinal colonisation by MDR E. coli ST131. To investigate the genetic basis of this superior gut colonisation ability by MDR E. coli, we assayed the metabolic capabilities of our strains using a Biolog phenotypic microarray revealing altered carbon metabolism. Functional pangenomic analysis of 19,571 E. coli genomes revealed that carriage of AMR genes is associated with increased diversity in carbohydrate metabolism genes. The data presented here demonstrate that independent of antibiotic selective pressures, MDR E. coli display a competitive advantage to colonise the mammalian gut and points to a vital role of metabolism in the evolution and success of MDR lineages of E. coli via carriage and spread.
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Affiliation(s)
- Christopher H. Connor
- Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
- International Microbiome Centre, University of Calgary, Calgary, Canada
| | - Amanda Z. Zucoloto
- International Microbiome Centre, University of Calgary, Calgary, Canada
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - John T. Munnoch
- Strathclyde Institute of Pharmaceutical and Biomedical Science, University of Strathclyde, Glasgow, United Kingdom
| | - Ian-Ling Yu
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Jukka Corander
- Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmaceutical and Biomedical Science, University of Strathclyde, Glasgow, United Kingdom
| | - Braedon McDonald
- International Microbiome Centre, University of Calgary, Calgary, Canada
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, United Kingdom
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Paulshus E, Colque P, Kühn I, Tauhid T, Hu YOO, Zhou Y, Thorell K, Möllby R, Sørum H, Sjöling Å, Joffré E. Escherichia coli ST2797 Is Abundant in Wastewater and Might Be a Novel Emerging Extended-Spectrum Beta-Lactamase E. coli. Microbiol Spectr 2023; 11:e0448622. [PMID: 37260395 PMCID: PMC10434162 DOI: 10.1128/spectrum.04486-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/17/2023] [Indexed: 06/02/2023] Open
Abstract
The increasing prevalence of antibiotic-resistant bacteria is an emerging threat to global health. The analysis of antibiotic-resistant enterobacteria in wastewater can indicate the prevalence and spread of certain clonal groups of multiresistant bacteria. In a previous study of Escherichia coli that were isolated from a pump station in Norway over 15 months, we found a recurring E. coli clone that was resistant to trimethoprim, ampicillin, and tetracycline in 201 of 3,123 analyzed isolates (6.1%). 11 representative isolates were subjected to whole-genome sequencing and were found to belong to the MLST ST2797 E. coli clone with plasmids carrying resistance genes, including blaTEM-1B, sul2, dfrA7, and tetB. A phenotypic comparison of the ST2797 isolates with the uropathogenic ST131 and ST648 that were repeatedly identified in the same wastewater samples revealed that the ST2797 isolates exhibited a comparable capacity for temporal survival in wastewater, greater biofilm formation, and similar potential for the colonization of mammalian epithelial cells. ST2797 has been isolated from humans and has been found to carry extended spectrum β-lactamase (ESBL) genes in other studies, suggesting that this clonal type is an emerging ESBL E. coli. Collectively, these findings show that ST2797 was more ubiquitous in the studied wastewater than were the infamous ST131 and ST648 and that ST2797 may have similar abilities to survive in the environment and cause infections in humans. IMPORTANCE The incidence of drug-resistant bacteria found in the environment is increasing together with the levels of antibiotic-resistant bacteria that cause infections. The COVID-19 pandemic has shed new light on the importance of monitoring emerging threats and finding early warning systems. Therefore, to mitigate the antimicrobial resistance burden, the monitoring and early identification of antibiotic-resistant bacteria in hot spots, such as wastewater treatment plants, are required to combat the occurrence and spread of antibiotic-resistant bacteria. Here, we applied a PhenePlate system as a phenotypic screening method for genomic surveillance and discovered a dominant and persistent E. coli clone ST2797 with a multidrug resistance pattern and equivalent phenotypic characteristics to those of the major pandemic lineages, namely, ST131 and ST648, which frequently carry ESBL genes. This study highlights the continuous surveillance and report of multidrug resistant bacteria with the potential to spread in One Health settings.
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Affiliation(s)
- Erik Paulshus
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Ås, Norway
| | - Patricia Colque
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Inger Kühn
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Tamanna Tauhid
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Yue O. O. Hu
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Yingshun Zhou
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- Department of Pathogen Biology, Southwest Medical University, Luzhou, Sichuan, China
| | - Kaisa Thorell
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Roland Möllby
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Henning Sørum
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Enrique Joffré
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
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7
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Zou Z, Potter RF, McCoy WH, Wildenthal JA, Katumba GL, Mucha PJ, Dantas G, Henderson JP. E. coli catheter-associated urinary tract infections are associated with distinctive virulence and biofilm gene determinants. JCI Insight 2023; 8:e161461. [PMID: 36512427 PMCID: PMC9977300 DOI: 10.1172/jci.insight.161461] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
Urinary catheterization facilitates urinary tract colonization by E. coli and increases infection risk. Here, we aimed to identify strain-specific characteristics associated with the transition from colonization to infection in catheterized patients. In a single-site study population, we compared E. coli isolates from patients with catheter-associated asymptomatic bacteriuria (CAASB) to those with catheter-associated urinary tract infection (CAUTI). CAUTI isolates were dominated by a phylotype B2 subclade containing the multidrug-resistant ST131 lineage relative to CAASB isolates, which were phylogenetically more diverse. A distinctive combination of virulence-associated genes was present in the CAUTI-associated B2 subclade. Catheter-associated biofilm formation was widespread among isolates and did not distinguish CAUTI from CAASB strains. Preincubation with CAASB strains could inhibit catheter colonization by multiple ST131 CAUTI isolates. Comparative genomic analysis identified a group of variable genes associated with high catheter biofilm formation present in both CAUTI and CAASB strains. Among these, ferric citrate transport (Fec) system genes were experimentally associated with enhanced catheter biofilm formation using reporter and fecA deletion strains. These results are consistent with a variable role for catheter biofilm formation in promoting CAUTI by ST131-like strains or resisting CAUTI by lower-risk strains that engage in niche exclusion.
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Affiliation(s)
- Zongsen Zou
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - Robert F. Potter
- The Edison Family Center for Genome Sciences and Systems Biology
- Department of Pathology and Immunology, and
| | - William H. McCoy
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Dermatology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John A. Wildenthal
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - George L. Katumba
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
| | - Peter J. Mucha
- Department of Mathematics, Dartmouth College, Hanover, New Hampshire, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology
- Department of Pathology and Immunology, and
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, Missouri, USA
| | - Jeffrey P. Henderson
- Center for Women’s Infectious Diseases Research
- Department of Internal Medicine, Division of Infectious Diseases
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8
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Zou M, Wang K, Zhao J, Lu H, Yang H, Huang M, Wang L, Wang G, Huang J, Min X. DegS protease regulates the motility, chemotaxis, and colonization of Vibrio cholerae. Front Microbiol 2023; 14:1159986. [PMID: 37089576 PMCID: PMC10113495 DOI: 10.3389/fmicb.2023.1159986] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023] Open
Abstract
In bacteria, DegS protease functions as an activating factor of the σE envelope stress response system, which ultimately activates the transcription of stress response genes in the cytoplasm. On the basis of high-throughput RNA sequencing, we have previously found that degS knockout inhibits the expression of flagellum synthesis- and chemotaxis-related genes, thereby indicating that DegS may be involved in the regulation of V. cholerae motility. In this study, we examined the relationships between DegS and motility in V. cholerae. Swimming motility and chemotaxis assays revealed that degS or rpoE deletion promotes a substantial reduction in the motility and chemotaxis of V. cholerae, whereas these activities were restored in ΔdegS::degS and ΔdegSΔrseA strains, indicating that DegS is partially dependent on σE to positively regulate V. cholerae activity. Gene-act network analysis revealed that the cAMP-CRP-RpoS signaling pathway, which plays an important role in flagellar synthesis, is significantly inhibited in ΔdegS mutants, whereas in response to the overexpression of cyaA/crp and rpoS in the ΔdegS strain, the motility and chemotaxis of the ΔdegS + cyaA/crp and ΔdegS + rpoS strains were partially restored compared with the ΔdegS strain. We further demonstrated that transcription levels of the flagellar regulatory gene flhF are regulated by DegS via the cAMP-CRP-RpoS signaling pathway. Overexpression of the flhF gene in the ΔdegS strain partially restored motility and chemotaxis. In addition, suckling mouse intestinal colonization experiments indicated that the ΔdegS and ΔrpoE strains were characterized by the poor colonization of mouse intestines, whereas colonization efficacy was restored in the ΔdegSΔrseA, ΔdegS + cyaA/crp, ΔdegS + rpoS, and ΔdegS + flhF strains. Collectively, our findings indicate that DegS regulates the motility and chemotaxis of V. cholerae via the cAMP-CRP-RpoS-FlhF pathway, thereby influencing the colonization of suckling mouse intestines.
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Affiliation(s)
- Mei Zou
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Kaiying Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jiajun Zhao
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Huifang Lu
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hui Yang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Meirong Huang
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
- Department of Blood Transfusion, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Lu Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Guangli Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jian Huang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xun Min
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
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9
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Schüroff PA, Abe CM, Silva JW, de Paula Coelho C, Andrade FB, Hernandes RT, Dobrindt U, Gomes TAT, Elias WP. Role of aggregate-forming pilus (AFP) in adherence and colonization of both intestinal and urinary tracts. Virulence 2022; 13:1423-1433. [PMID: 35982607 PMCID: PMC9397481 DOI: 10.1080/21505594.2022.2112818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hybrid-pathogenic Escherichia coli represent an important group of strains associated with intestinal and extraintestinal infections. Recently, we described strain UPEC-46, a uropathogenic/enteroaggregative E. coli (UPEC/EAEC) strain presenting the aggregative adherence (AA) pattern on bladder and colorectal epithelial cells mediated by aggregate-forming pili (AFP). However, the role of AFP and other uninvestigated putative fimbriae operons in UPEC-46 pathogenesis remains unclear. Thus, this study evaluated the involvement of AFP and other adhesins in uropathogenicity and intestinal colonization using different in vitro and in vivo models. The strain UPEC-46 was able to adhere and invade intestinal and urinary cell lines. A library of transposon mutants also identified the involvement of type I fimbriae (TIF) in the adherence to HeLa cells, in addition to colorectal and bladder cell lines. The streptomycin-treated mouse in vivo model also showed an increased number of bacterial counts in the colon in the presence of AFP and TIF. In the mouse model of ascending urinary tract infection (UTI), AFP was more associated with kidney colonization, while TIF appears to mediate bladder colonization. Results observed in in vivo experiments were also confirmed by electron microscopy (EM) analyses. In summary, the in vitro and in vivo analyses show a synergistic role of AFP and TIF in the adherence and colonization of intestinal and urinary epithelia. Therefore, we propose that hybrid E. coli strains carrying AFP and TIF could potentially cause intestinal and urinary tract infections in the same patient.
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Affiliation(s)
- Paulo A Schüroff
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil.,Institute of Hygiene, University of Münster, Münster, Germany
| | - Cecilia M Abe
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Jonatas W Silva
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Cidéli de Paula Coelho
- Departamento de Pós-graduação, Faculdade de Medicina Veterinária, Universidade Santo Amaro, São Paulo, Brazil
| | | | - Rodrigo T Hernandes
- Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, Brazil
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Tânia A T Gomes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Waldir P Elias
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
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10
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Loss of β-Ketoacyl Acyl Carrier Protein Synthase III Activity Restores Multidrug-Resistant Escherichia coli Sensitivity to Previously Ineffective Antibiotics. mSphere 2022; 7:e0011722. [PMID: 35574679 PMCID: PMC9241538 DOI: 10.1128/msphere.00117-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gram-negative pathogens are a major concern for global public health due to increasing rates of antibiotic resistance and the lack of new drugs. A major contributing factor toward antibiotic resistance in Gram-negative bacteria is their formidable outer membrane, which acts as a permeability barrier preventing many biologically active antimicrobials from reaching the intracellular targets and thus limiting their efficacy.
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11
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Godijk NG, Bootsma MCJ, van Werkhoven HC, Schweitzer VA, de Greeff SC, Schoffelen AF, Bonten MJM. Does plasmid-based beta-lactam resistance increase E. coli infections: Modelling addition and replacement mechanisms. PLoS Comput Biol 2022; 18:e1009875. [PMID: 35286302 PMCID: PMC8947615 DOI: 10.1371/journal.pcbi.1009875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 03/24/2022] [Accepted: 01/27/2022] [Indexed: 11/19/2022] Open
Abstract
Infections caused by antibiotic-resistant bacteria have become more prevalent during past decades. Yet, it is unknown whether such infections occur in addition to infections with antibiotic-susceptible bacteria, thereby increasing the incidence of infections, or whether they replace such infections, leaving the total incidence unaffected. Observational longitudinal studies cannot separate both mechanisms. Using plasmid-based beta-lactam resistant E. coli as example we applied mathematical modelling to investigate whether seven biological mechanisms would lead to replacement or addition of infections. We use a mathematical neutral null model of individuals colonized with susceptible and/or resistant E. coli, with two mechanisms implying a fitness cost, i.e., increased clearance and decreased growth of resistant strains, and five mechanisms benefitting resistance, i.e., 1) increased virulence, 2) increased transmission, 3) decreased clearance of resistant strains, 4) increased rate of horizontal plasmid transfer, and 5) increased clearance of susceptible E. coli due to antibiotics. Each mechanism is modelled separately to estimate addition to or replacement of antibiotic-susceptible infections. Fitness costs cause resistant strains to die out if other strain characteristics are maintained equal. Under the assumptions tested, increased virulence is the only mechanism that increases the total number of infections. Other benefits of resistance lead to replacement of susceptible infections without changing the total number of infections. As there is no biological evidence that plasmid-based beta-lactam resistance increases virulence, these findings suggest that the burden of disease is determined by attributable effects of resistance rather than by an increase in the number of infections.
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Affiliation(s)
- Noortje G. Godijk
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- * E-mail:
| | - Martin C. J. Bootsma
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Mathematics, Faculty of Sciences, Utrecht University, Utrecht, the Netherlands
| | - Henri C. van Werkhoven
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Valentijn A. Schweitzer
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sabine C. de Greeff
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Annelot F. Schoffelen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Marc J. M. Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
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12
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Kondo T, Sakamoto K, Morinaga Y, Miyata Y, Yanagihara K, Sakai H. Escherichia coli ST131 isolated from urological patients can acquire plasmid-mediated extended spectrum β-lactamase from other bacteria with high frequency. Int J Urol 2022; 29:587-594. [PMID: 35288997 DOI: 10.1111/iju.14845] [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: 09/06/2021] [Accepted: 02/20/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To investigate the prevalence of the clonal group Escherichia coli ST131 in urologic patients, and to clarify the mechanisms underlying the high prevalence of the antimicrobial resistant genes in ST131. METHODS We used 65 Escherichia coli strains collected from the Department of Urology, Nagasaki University Hospital, between January 2018 and December 2018. All of them underwent multilocus sequence typing and were analyzed for genes associated with quinolone resistance and extended-spectrum β-lactamases. To compare ST131 and non-ST131 strains, bacterial conjugation experiments and intestinal colonization evaluations were performed. RESULTS ST131 was the most dominant among all the strains, along with levofloxacin resistant strains, and extended-spectrum β-lactamases positive strains (32%, 63%, and 73%, respectively). 12 out of 15 extended-spectrum β-lactamases-producing Escherichia coli strains harbored CTX-M-9. In particular, all extended-spectrum β-lactamases-producing ST131 strains possessed CTX-M-9. The proportions of ST131 strains with or without quinolone resistance-determining region mutations were significantly higher and lower, respectively, than that of non-ST131 strains (P = 0.0002 and P < 0.0001, respectively). When Klebsiella pneumoniae was used as a donor, three ST131 strains acquired extended-spectrum β-lactamases a total of 16 times (six, four, and six times each), which was significantly more than that in one of the non-ST131 strains (two times). The amount of bacteria was significantly lower in the ST131 strains than in the non-ST131 strains administered to mice. Both the ST131 and non-ST131 strains increased again after the administration of vancomycin, even after the colony was not detected. CONCLUSIONS These results support the mechanisms underlying the prevalence of ST131 strains in hospitals, particularly in urologic patients.
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Affiliation(s)
- Tsubasa Kondo
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kei Sakamoto
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yoshitomo Morinaga
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yasuyoshi Miyata
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hideki Sakai
- Department of Urology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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13
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Abstract
Urinary tract infection (UTI) is the most common type of urogenital disease. UTI affects the urethra, bladder, ureter, and kidney. A total of 13.3% of women, 2.3% of men, and 3.4% of children in the United States will require treatment for UTI. Traditionally, bladder (cystitis) and kidney (pyelonephritis) infections are considered independently. However, both infections induce host defenses that are either shared or coordinated across the urinary tract. Here, we review the chemical and biophysical mechanisms of bacteriostasis, which limit the duration and severity of the illness. Urinary bacteria attempt to overcome each of these defenses, complicating description of the natural history of UTI.
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Affiliation(s)
| | - Anne-Catrin Uhlemann
- Department of Medicine and Pathology and Urology, Columbia University, New York, NY, USA;
| | - Jonathan Barasch
- Department of Medicine and Pathology and Urology, Columbia University, New York, NY, USA;
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14
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Tsoumtsa Meda LL, Landraud L, Petracchini S, Descorps-Declere S, Perthame E, Nahori MA, Ramirez Finn L, Ingersoll MA, Patiño-Navarrete R, Glaser P, Bonnet R, Dussurget O, Denamur E, Mettouchi A, Lemichez E. The cnf1 gene is associated with an expanding Escherichia coli ST131 H30Rx/C2 subclade and confers a competitive advantage for gut colonization. Gut Microbes 2022; 14:2121577. [PMID: 36154446 PMCID: PMC9519008 DOI: 10.1080/19490976.2022.2121577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/30/2022] [Indexed: 02/04/2023] Open
Abstract
Epidemiological projections point to acquisition of ever-expanding multidrug resistance (MDR) by Escherichia coli, a commensal of the digestive tract and a source of urinary tract pathogens. Bioinformatics analyses of a large collection of E. coli genomes from EnteroBase, enriched in clinical isolates of worldwide origins, suggest the Cytotoxic Necrotizing Factor 1 (CNF1)-toxin encoding gene, cnf1, is preferentially distributed in four common sequence types (ST) encompassing the pandemic E. coli MDR lineage ST131. This lineage is responsible for a majority of extraintestinal infections that escape first-line antibiotic treatment, with known enhanced capacities to colonize the gastrointestinal tract. Statistical projections based on this dataset point to a global expansion of cnf1-positive multidrug-resistant ST131 strains from subclade H30Rx/C2, accounting for a rising prevalence of cnf1-positive strains in ST131. Despite the absence of phylogeographical signals, cnf1-positive isolates segregated into clusters in the ST131-H30Rx/C2 phylogeny, sharing a similar profile of virulence factors and the same cnf1 allele. The suggested dominant expansion of cnf1-positive strains in ST131-H30Rx/C2 led us to uncover the competitive advantage conferred by cnf1 for gut colonization to the clinical strain EC131GY ST131-H30Rx/C2 versus cnf1-deleted isogenic strain. Complementation experiments showed that colon tissue invasion was compromised in the absence of deamidase activity on Rho GTPases by CNF1. Hence, gut colonization factor function of cnf1 was confirmed for another clinical strain ST131-H30Rx/C2. In addition, functional analysis of the cnf1-positive clinical strain EC131GY ST131-H30Rx/C2 and a cnf1-deleted isogenic strain showed no detectable impact of the CNF1 gene on bacterial fitness and inflammation during the acute phase of bladder monoinfection. Together these data argue for an absence of role of CNF1 in virulence during UTI, while enhancing gut colonization capacities of ST131-H30Rx/C2 and suggested expansion of cnf1-positive MDR isolates in subclade ST131-H30Rx/C2.
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Affiliation(s)
- Landry L. Tsoumtsa Meda
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France
| | - Luce Landraud
- Université Paris Cité et Université Sorbonne Paris Nord, INSERM U1137, IAME, Paris, France
- Laboratoire Microbiologie-hygiène, AP-HP, Hôpital Louis Mourier, Colombes, France
| | - Serena Petracchini
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France
| | - Stéphane Descorps-Declere
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Emeline Perthame
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Marie-Anne Nahori
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France
| | - Laura Ramirez Finn
- Institut Pasteur, Department of Immunology, Mucosal Inflammation and Immunity group, Paris, France
- Université Paris Cité, Institut Cochin, CNRS UMR8104, INSERM U1016, Paris, France
| | - Molly A. Ingersoll
- Institut Pasteur, Department of Immunology, Mucosal Inflammation and Immunity group, Paris, France
- Université Paris Cité, Institut Cochin, CNRS UMR8104, INSERM U1016, Paris, France
| | - Rafael Patiño-Navarrete
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Département de Microbiologie, Paris, France
| | - Philippe Glaser
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Département de Microbiologie, Paris, France
| | - Richard Bonnet
- UMR INSERM U1071, INRA USC-2018, Université Clermont Auvergne, Clermont-Ferrand, France
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire, Clermont-Ferrand, France
| | - Olivier Dussurget
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unité de Recherche Yersinia, Département de Microbiologie, Paris, France
| | - Erick Denamur
- Université Paris Cité et Université Sorbonne Paris Nord, INSERM U1137, IAME, Paris, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Amel Mettouchi
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France
| | - Emmanuel Lemichez
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité des Toxines Bactériennes, Département de Microbiologie, Paris, France
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15
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Fukuda A, Nakamura H, Umeda K, Yamamoto K, Hirai Y, Usui M, Ogasawara J. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac031. [PMID: 35350135 PMCID: PMC8952253 DOI: 10.1093/jacamr/dlac031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Hiromi Nakamura
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Kaoru Umeda
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Kaori Yamamoto
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yuji Hirai
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Masaru Usui
- Food Microbiology and Food Safety Unit, Division of Preventive Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Jun Ogasawara
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
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16
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Qin J, Wilson KA, Sarkar S, Heras B, O'Mara ML, Totsika M. Conserved FimH mutations in the global Escherichia coli ST131 multi-drug resistant lineage weaken interdomain interactions and alter adhesin function. Comput Struct Biotechnol J 2022; 20:4532-4541. [PMID: 36090810 PMCID: PMC9428848 DOI: 10.1016/j.csbj.2022.08.040] [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: 05/19/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/27/2022] Open
Abstract
The binding of the type 1 fimbrial adhesin FimH to mannosylated receptors is allosterically regulated to enhance the fitness of uropathogenic Escherichia coli (UPEC) during urinary tract infection (UTI). Mutations in the two FimH domains (pilin and lectin) located outside the mannose binding pocket have been shown to influence mannose binding affinity, yet the details of the allostery mechanism are not fully elucidated. Here we characterised different FimH conformational states (termed low-affinity tense and high-affinity relaxed conformations) of natural FimH variants using molecular dynamics (MD) simulation techniques and report key structural dynamics differences between them. The clinically dominant FimH30 variant from the pandemic multidrug resistant E. coli ST131 lineage contains an R166H mutation that weakens FimH interdomain interactions and allows enhanced mannose interactions with pre-existing high-affinity relaxed conformations. When expressed in an isogenic ST131 strain background, FimH30 mediated high human cell adhesion and invasion, and enhanced biofilm formation over other variants. Collectively, our computational and experimental findings support a model of FimH protein allostery that is mediated by shifts in the pre-existing conformational equilibrium of FimH, additional to the sequential step-wise process of structural perturbations transmitted from one site to another within the protein. Importantly, it is the first study to shed light into how natural mutations in a clinically dominant FimH variant influence the protein’s conformational landscape optimising its function for ST131 fitness at intestinal and extraintestinal niches.
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17
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A 21-Year Survey of Escherichia coli from Bloodstream Infections (BSI) in a Tertiary Hospital Reveals How Community-Hospital Dynamics of B2 Phylogroup Clones Influence Local BSI Rates. mSphere 2021; 6:e0086821. [PMID: 34935444 PMCID: PMC8722714 DOI: 10.1128/msphere.00868-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This is a longitudinal study comprising 649 Escherichia coli isolates representing all 7,165 E. coli bloodstream infection (BSI) episodes recorded in a hospital (1996 to 2016). Strain analysis included clonal identification (phylogenetic groups/subgroups, STc131 subclades, pulsed-field gel electrophoresis [PFGE], and whole-genome sequencing [WGS]), antibiotic susceptibility (13 antibiotics), and virulence-associated genes (VAGs; 29 genes). The incidence of E. coli BSI increased from 1996 to 2016 (5.5 to 10.8 BSI episodes/1,000 hospitalizations, average 7 to 8/1,000). B2 isolates predominate (53%), with subgroups B2-I (STc131), B2-II, B2-IX, and B2-VI representing 25%, 25%, 14%, and 9%, respectively. Intertwined waves of community-acquired (CA) plus health care-associated and community-onset health care-associated (HCA) and hospital-acquired (HA) episodes of both B2 and non-B2 phylogroups occurred. A remarkable increase was observed only for B2-I-STc131 (C1/C2 subclades), with oscillations for other B2 subgroups and phylogroups throughout the years. Epidemic and persistent clones (comprising isolates with highly similar/identical PFGE types and genomes differing in 6 to 173 single nucleotide polymorphisms [SNPs]) of B2-I (STc131), B2-II (STc73), B2-III (STc127), B2-IX (STc95), and B2-VI (STc12) were recovered from different patients, most at hospital admission, for long periods (2 to 17 years), and extended-spectrum beta-lactamase (ESBL) producers or resistance to ciprofloxacin in B2 isolates was almost restricted to B2-I (STc131) subclade C. STc131 contributed to increasing the B2 rates but only transiently altered the E. coli population structure. The increase of E. coli BSI was determined by waves of CA+HCA BSI episodes that predate the waves of HA BSI. Besides the risk of hospital transmission that led to temporal increases in BSI, this study suggests that E. coli populations/clones from community-based healthy individuals may occasionally have an epidemic structure and provide a source of transmissible strains influencing the HA BSI incidence. IMPORTANCE Sepsis is the third leading cause of mortality in Western countries and one of the Global Health Threats recognized by the WHO since 2017. Despite Escherichia coli constituting the most common cause of bloodstream infections (BSI), its epidemiology is not fully understood, in part due to the scarcity of local and longitudinal studies. Our work analyzes the long-term dynamics of E. coli causing bacteremia in a single institution and reveals waves of different clonal lineages that emerge periodically and successfully spread afterward in both the community and hospitals. Because the origin of E. coli bloodstream infections is the gut, the microbiota of healthy individuals might occasionally have an epidemic structure, providing a source of E. coli strains to influence the incidence of hospital BSI. The study complements previous fractionated observations focusing on specific E. coli lineages or antibiotic-resistant isolates in the last decades and helps to understand the epidemiology of E. coli BSI and the dynamics of pandemic clones.
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18
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Karpe AV, Hutton ML, Mileto SJ, James ML, Evans C, Shah RM, Ghodke AB, Hillyer KE, Metcalfe SS, Liu JW, Walsh T, Lyras D, Palombo EA, Beale DJ. Cryptosporidiosis Modulates the Gut Microbiome and Metabolism in a Murine Infection Model. Metabolites 2021; 11:metabo11060380. [PMID: 34208228 PMCID: PMC8230837 DOI: 10.3390/metabo11060380] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Cryptosporidiosis is a major human health concern globally. Despite well-established methods, misdiagnosis remains common. Our understanding of the cryptosporidiosis biochemical mechanism remains limited, compounding the difficulty of clinical diagnosis. Here, we used a systems biology approach to investigate the underlying biochemical interactions in C57BL/6J mice infected with Cryptosporidium parvum. Faecal samples were collected daily following infection. Blood, liver tissues and luminal contents were collected 10 days post infection. High-resolution liquid chromatography and low-resolution gas chromatography coupled with mass spectrometry were used to analyse the proteomes and metabolomes of these samples. Faeces and luminal contents were additionally subjected to 16S rRNA gene sequencing. Univariate and multivariate statistical analysis of the acquired data illustrated altered host and microbial energy pathways during infection. Glycolysis/citrate cycle metabolites were depleted, while short-chain fatty acids and D-amino acids accumulated. An increased abundance of bacteria associated with a stressed gut environment was seen. Host proteins involved in energy pathways and Lactobacillus glyceraldehyde-3-phosphate dehydrogenase were upregulated during cryptosporidiosis. Liver oxalate also increased during infection. Microbiome–parasite relationships were observed to be more influential than the host–parasite association in mediating major biochemical changes in the mouse gut during cryptosporidiosis. Defining this parasite–microbiome interaction is the first step towards building a comprehensive cryptosporidiosis model towards biomarker discovery, and rapid and accurate diagnostics.
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Affiliation(s)
- Avinash V. Karpe
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; (A.V.K.); (R.M.S.); (K.E.H.); (S.S.M.)
| | - Melanie L. Hutton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (M.L.H.); (S.J.M.); (M.L.J.); (C.E.); (D.L.)
| | - Steven J. Mileto
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (M.L.H.); (S.J.M.); (M.L.J.); (C.E.); (D.L.)
| | - Meagan L. James
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (M.L.H.); (S.J.M.); (M.L.J.); (C.E.); (D.L.)
| | - Chris Evans
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (M.L.H.); (S.J.M.); (M.L.J.); (C.E.); (D.L.)
| | - Rohan M. Shah
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; (A.V.K.); (R.M.S.); (K.E.H.); (S.S.M.)
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia;
| | - Amol B. Ghodke
- Queensland Alliance for Agriculture and Food Innovation, Department of Horticulture, The University of Queensland, St Lucia, QLD 4072, Australia;
- BIO21 Institute, School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Katie E. Hillyer
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; (A.V.K.); (R.M.S.); (K.E.H.); (S.S.M.)
| | - Suzanne S. Metcalfe
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; (A.V.K.); (R.M.S.); (K.E.H.); (S.S.M.)
| | - Jian-Wei Liu
- Land and Water, Commonwealth Scientific and Industrial Research Organization Research and Innovation Park, Acton, ACT 2601, Australia; (J.-W.L.); (T.W.)
| | - Tom Walsh
- Land and Water, Commonwealth Scientific and Industrial Research Organization Research and Innovation Park, Acton, ACT 2601, Australia; (J.-W.L.); (T.W.)
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (M.L.H.); (S.J.M.); (M.L.J.); (C.E.); (D.L.)
| | - Enzo A. Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia;
| | - David J. Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia; (A.V.K.); (R.M.S.); (K.E.H.); (S.S.M.)
- Correspondence: ; Tel.: +61-7-3833-5774
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19
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Taati Moghadam M, Mirzaei M, Fazel Tehrani Moghaddam M, Babakhani S, Yeganeh O, Asgharzadeh S, Farahani HE, Shahbazi S. The Challenge of Global Emergence of Novel Colistin-Resistant Escherichia coli ST131. Microb Drug Resist 2021; 27:1513-1524. [PMID: 33913748 DOI: 10.1089/mdr.2020.0505] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Escherichia coli ST131 is one of the high-risk multidrug-resistant clones with a global distribution and the ability to persist and colonize in a variety of niches. Carbapenemase-producing E. coli ST131 strains with the ability to resist last-line antibiotics (i.e., colistin) have been recently considered a significant public health. Colistin is widely used in veterinary medicine and therefore, colistin-resistant bacteria can be transmitted from livestock to humans through food. There are several mechanisms of resistance to colistin, which include chromosomal mutations and plasmid-transmitted mcr genes. E. coli ST131 is a great model organism to investigate the emergence of superbugs. This microorganism has the ability to cause intestinal and extraintestinal infections, and its accurate identification as well as its antibiotic resistance patterns are vitally important for a successful treatment strategy. Therefore, further studies are required to understand the evolution of this resistant organism for drug design, controlling the evolution of other nascent emerging pathogens, and developing antibiotic stewardship programs. In this review, we will discuss the importance of E. coli ST131, the mechanisms of resistance to colistin as the last-resort antibiotic against resistant Gram-negative bacteria, reports from different regions regarding E. coli ST131 resistance to colistin, and the most recent therapeutic approaches against colistin-resistance bacteria.
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Affiliation(s)
- Majid Taati Moghadam
- Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, Iran University of Medical Sciences, Tehran, Iran
| | - Mehrnaz Mirzaei
- Department of Microbiology, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | | | - Sajad Babakhani
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Omid Yeganeh
- Department of Microbiology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Sajad Asgharzadeh
- Department of Microbiology, Iran University of Medical Sciences, Tehran, Iran
| | | | - Shahla Shahbazi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
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20
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Damalanka VC, Maddirala AR, Janetka JW. Novel approaches to glycomimetic design: development of small molecular weight lectin antagonists. Expert Opin Drug Discov 2021; 16:513-536. [PMID: 33337918 DOI: 10.1080/17460441.2021.1857721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introduction: The direct binding of carbohydrates or those presented on glycoproteins or glycolipids to proteins is the primary effector of many biological responses. One class of carbohydrate-binding proteins, lectins are important in all forms of life. Their functions in animals include regulating cell adhesion, glycoprotein synthesis, metabolism, and mediating immune system response while in bacteria and viruses a lectin-mediated carbohydrate-protein interaction between host cells and the pathogen initiates pathogenesis of the infection.Areas covered: In this review, the authors outline the structural and functional pathogenesis of lectins from bacteria, amoeba, and humans. Mimics of a carbohydrate are referred to as glycomimetics, which are much smaller in molecular weight and are devised to mimic the key binding interactions of the carbohydrate while also allowing additional contacts with the lectin. This article emphasizes the various approaches used over the past 10-15 years in the rational design of glycomimetic ligands.Expert opinion: Medicinal chemistry efforts enabled by X-ray structural biology have identified small-molecule glycomimetic lectin antagonists that have entered or are nearing clinical trials. A common theme in these strategies is the use of biaryl ring systems to emulate the carbohydrate interactions with the lectin.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
| | - Amarendar Reddy Maddirala
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
| | - James W Janetka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
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21
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Johnson TJ. Role of Plasmids in the Ecology and Evolution of "High-Risk" Extraintestinal Pathogenic Escherichia coli Clones. EcoSal Plus 2021; 9:eESP-0013-2020. [PMID: 33634776 PMCID: PMC11163845 DOI: 10.1128/ecosalplus.esp-0013-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/12/2021] [Indexed: 11/20/2022]
Abstract
Bacterial plasmids have been linked to virulence in Escherichia coli and Salmonella since their initial discovery. Though the plasmid repertoire of these bacterial species is extremely diverse, virulence-associated attributes tend to be limited to a small subset of plasmid types. This is particularly true for extraintestinal pathogenic E. coli, or ExPEC, where a handful of plasmids have been recognized to confer virulence- and fitness-associated traits. The purpose of this review is to highlight the biological and genomic attributes of ExPEC virulence-associated plasmids, with an emphasis on high-risk dominant ExPEC clones. Two specific plasmid types are highlighted to illustrate the independently evolved commonalities of these clones relative to plasmid content. Furthermore, the dissemination of these plasmids within and between bacterial species is examined. These examples demonstrate the evolution of high-risk clones toward common goals, and they show that rare transfer events can shape the ecological landscape of dominant clones within a pathotype.
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Affiliation(s)
- Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108
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22
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Chen WC, Hung CH, Chen YS, Cheng JS, Lee SSJ, Tseng FC, Cheng MF, Wang JL. Bloodstream Infections Caused by Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Patients with Liver Cirrhosis. Pathogens 2021; 10:pathogens10010037. [PMID: 33466521 PMCID: PMC7824895 DOI: 10.3390/pathogens10010037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022] Open
Abstract
Background: This study aimed to investigate the frequency of sequence type (ST) 131 strains and outcome of cirrhotic patients with bloodstream infections (BSIs) caused by extended-spectrum beta-lactamase-producing Escherichiacoli (ESBLEC) and non-extended-spectrum beta-lactamase-producing Escherichiacoli (NESBLEC). Methods: The incidence of ST 131 strains, hospital stay, and 30-day re-admission/mortality were compared between 51 ESBLEC and 51 NESBLEC bacteremic patients with cirrhosis. Results: ST 131 strains were found in 35.3% of the ESBLEC group and 0% of the NESBLEC group (p < 0.001). Mean hospital stay was 26.5 days in the ESBLEC group and 17.1 days in the NESBLEC group (p = 0.006). Thirty-day re-admission rates were 11.8% in the ESBLEC group and 5.9% in the NESBLEC group (p = 0.5). ST 131 strains were associated with 30-day re-admission (odds ratio: 4.5, 95% confidence interval: 1.1–18.9). Thirty-day mortality rate was 31.4% in the ESBLEC group and 23.5% in the NESBLEC group (p = 0.4). Conclusion: In patients with cirrhosis, the ESBLEC BSIs group had a higher frequency of ST 131 strains and longer hospital stay than the NESBLEC BSIs group with similar 30-day re-admission/mortality. ST 131 strains were associated with 30-day re-admission.
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Affiliation(s)
- Wen-Chi Chen
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kaohsiung Veterans General Hospital and School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (W.-C.C.); (J.-S.C.)
| | - Chih-Hsin Hung
- Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung 840, Taiwan;
| | - Yao-Shen Chen
- Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Veterans General Hospital and School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (Y.-S.C.); (S.S.-J.L.)
| | - Jin-Shiung Cheng
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kaohsiung Veterans General Hospital and School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (W.-C.C.); (J.-S.C.)
| | - Susan Shin-Jung Lee
- Division of Infectious Disease, Department of Internal Medicine, Kaohsiung Veterans General Hospital and School of Medicine, National Yang-Ming University, Taipei 112, Taiwan; (Y.-S.C.); (S.S.-J.L.)
| | - Fan-Chen Tseng
- Graduate Institute of Basic Medical Science, China Medical University and Department of Nursing, National Taipei University of Nursing and Health Sciences, Taipei 112, Taiwan;
| | - Ming-Fang Cheng
- Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung 840, Taiwan;
- Department of Pediatrics, Kaohsiung Veterans General Hospital and School of Medicine, Kaohsiung 813, Taiwan
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan
- Department of Nursing, Fooyin University, Kaohsiung 831, Taiwan
- Correspondence: (M.-F.C.); (J.-L.W.); Tel.: +886-7-3468203 (M.-F.C.); +886-6-2757575 (J.-L.W.); Fax: +886-7-3468207 (M.-F.C.); +886-6-2766175 (J.-L.W.)
| | - Jiun-Ling Wang
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan
- Department of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Correspondence: (M.-F.C.); (J.-L.W.); Tel.: +886-7-3468203 (M.-F.C.); +886-6-2757575 (J.-L.W.); Fax: +886-7-3468207 (M.-F.C.); +886-6-2766175 (J.-L.W.)
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23
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Mota R, Pinto M, Palmeira J, Gonçalves D, Ferreira H. Multidrug-resistant bacteria as intestinal colonizers and evolution of intestinal colonization in healthy university students in Portugal. Access Microbiol 2020; 3:acmi000182. [PMID: 33997613 PMCID: PMC8115976 DOI: 10.1099/acmi.0.000182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/02/2020] [Indexed: 12/18/2022] Open
Abstract
Multidrug-resistant bacteria have been increasingly described in healthcare institutions, however community resistance also seems to be emerging. Escherichia coli an intestinal commensal bacteria, is also a pathogen and represents an important intestinal reservoir of resistance. Our aim was the study of the intestinal colonization and of the persistence of antibiotic resistant intestinal bacteria in healthy university students of Porto, in the north of Portugal. Samples from 30 university students were collected and analysed. Two E. coli isolates were randomly obtained from each student and Gram-negative bacilli resistant to antibiotics were studied. In addition, we evaluated changes in the Gram-negative intestinal colonization of ten university students in a short period of time. Molecular characterization showed a high presence of bla TEM in commensal E. coli . Gram-negative bacteria with intrinsic and extrinsic resistance were isolated, namely Pseudomonas spp., Enterobacter spp. and Pantoea spp. We isolated three ESBL-producing E. coli from two students. These isolates showed bla CTX-M group 1 (n=1), bla CTX-M group 9 (n=2), bla TEM (n=2), bla SHV (n=1) and tetA (n=2) genes. Additionally, they showed specific virulence factors and conjugational transfer of antibiotic resistance and virulence genes. One Pseudomonas spp. isolate resistant to carbapenems was detected colonizing one student. Our results confirm that healthy young adults may be colonized with commensals showing clinically relevant antibiotic resistance mechanisms, creating a risk of silent spread of these bacteria in the community.
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Affiliation(s)
- Raquel Mota
- UCIBIO, Microbiology, Faculty of Pharmacy of University of Porto, Portugal.,Microbiology, Faculty of Pharmacy of University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Marisa Pinto
- UCIBIO, Microbiology, Faculty of Pharmacy of University of Porto, Portugal.,Microbiology, Faculty of Pharmacy of University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Josman Palmeira
- UCIBIO, Microbiology, Faculty of Pharmacy of University of Porto, Portugal.,Microbiology, Faculty of Pharmacy of University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Daniela Gonçalves
- UCIBIO, Microbiology, Faculty of Pharmacy of University of Porto, Portugal.,Microbiology, Faculty of Pharmacy of University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.,Instituto Superior de Saúde, Rua Castelo de Almourol, 4720-155 Amares, Portugal
| | - Helena Ferreira
- UCIBIO, Microbiology, Faculty of Pharmacy of University of Porto, Portugal.,Microbiology, Faculty of Pharmacy of University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
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24
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Abstract
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.
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25
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Phenotypic Parallelism during Experimental Adaptation of a Free-Living Bacterium to the Zebrafish Gut. mBio 2020; 11:mBio.01519-20. [PMID: 32817106 PMCID: PMC7439477 DOI: 10.1128/mbio.01519-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although animals encounter many bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. We used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association. Although animals encounter a plethora of bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. However, our understanding of how bacteria initiate symbioses with animal hosts remains underexplored, and this process is central to the assembly and function of gut bacterial communities. Therefore, we used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). After approximately 200 bacterial generations, isolates from evolved populations improved their ability to colonize larval zebrafish during competition against their unpassaged ancestor. Genome sequencing revealed unique sets of mutations in the two evolved isolates exhibiting the highest mean competitive fitness. One isolate exhibited increased swimming motility and decreased biofilm formation compared to the ancestor, and we identified a missense mutation in the mannose-sensitive hemagglutinin pilus operon that is sufficient to increase fitness and reproduce these phenotypes. The second isolate exhibited enhanced swimming motility but unchanged biofilm formation, and here the genetic basis for adaptation is less clear. These parallel enhancements in motility and fitness resemble the behavior of a closely related Shewanella strain previously isolated from larval zebrafish and suggest phenotypic convergence with this isolate. Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association.
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26
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Whitmer GR, Moorthy G, Arshad M. The pandemic Escherichia coli sequence type 131 strain is acquired even in the absence of antibiotic exposure. PLoS Pathog 2019; 15:e1008162. [PMID: 31856254 PMCID: PMC6922328 DOI: 10.1371/journal.ppat.1008162] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Grant R. Whitmer
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Ganga Moorthy
- Department of Pediatrics, Duke University, Durham, North Carolina, United States of America
| | - Mehreen Arshad
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Pediatrics, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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27
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Intestinal cytotoxicity induced by Escherichia coli is fully prevented by red wine polyphenol extract: Mechanistic insights in epithelial cells. Chem Biol Interact 2019; 310:108711. [DOI: 10.1016/j.cbi.2019.06.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/08/2019] [Accepted: 06/11/2019] [Indexed: 12/14/2022]
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28
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Population dynamics of an Escherichia coli ST131 lineage during recurrent urinary tract infection. Nat Commun 2019; 10:3643. [PMID: 31409795 PMCID: PMC6692316 DOI: 10.1038/s41467-019-11571-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/16/2019] [Indexed: 12/31/2022] Open
Abstract
Recurrent urinary tract infections (rUTIs) are extremely common, with ~ 25% of all women experiencing a recurrence within 1 year of their original infection. Escherichia coli ST131 is a globally dominant multidrug resistant clone associated with high rates of rUTI. Here, we show the dynamics of an ST131 population over a 5-year period from one elderly woman with rUTI since the 1970s. Using whole genome sequencing, we identify an indigenous clonal lineage (P1A) linked to rUTI and persistence in the fecal flora, providing compelling evidence of an intestinal reservoir of rUTI. We also show that the P1A lineage possesses substantial plasmid diversity, resulting in the coexistence of antibiotic resistant and sensitive intestinal isolates despite frequent treatment. Our longitudinal study provides a unique comprehensive genomic analysis of a clonal lineage within a single individual and suggests a population-wide resistance mechanism enabling rapid adaptation to fluctuating antibiotic exposure. Recurrent urinary tract infections occur in ~ 25% of women. Here, Beatson and colleagues use whole genome sequencing to track the dynamics of an E. coli ST131 clone in a single patient over a 5-year period. This study provides unique insights into pathogen evolution during recurrent urinary infection.
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29
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Tamadonfar KO, Omattage NS, Spaulding CN, Hultgren SJ. Reaching the End of the Line: Urinary Tract Infections. Microbiol Spectr 2019; 7:10.1128/microbiolspec.bai-0014-2019. [PMID: 31172909 PMCID: PMC11314827 DOI: 10.1128/microbiolspec.bai-0014-2019] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Indexed: 12/26/2022] Open
Abstract
Urinary tract infections (UTIs) cause a substantial health care burden. UTIs (i) are most often caused by uropathogenic Escherichia coli (UPEC), (ii) primarily affect otherwise healthy females (50% of women will have a UTI), (iii) are associated with significant morbidity and economic impact, (iv) can become chronic, and (v) are highly recurrent. A history of UTI is a significant risk factor for a recurrent UTI (rUTI). In otherwise healthy women, an acute UTI leads to a 25 to 50% chance of rUTI within months of the initial infection. Interestingly, rUTIs are commonly caused by the same strain of E. coli that led to the initial infection, arguing that there exist host-associated reservoirs, like the gastrointestinal tract and underlying bladder tissue, that can seed rUTIs. Additionally, catheter-associated UTIs (CAUTI), caused by Enterococcus and Staphylococcus as well as UPEC, represent a major health care concern. The host's response of depositing fibrinogen at the site of infection has been found to be critical to establishing CAUTI. The Drug Resistance Index, an evaluation of antibiotic resistance, indicates that UTIs have become increasingly difficult to treat since the mid-2000s. Thus, UTIs are a "canary in the coal mine," warning of the possibility of a return to the preantibiotic era, where some common infections are untreatable with available antibiotics. Numerous alternative strategies for both the prevention and treatment of UTIs are being pursued, with a focus on the development of vaccines and small-molecule inhibitors targeting virulence factors, in the hopes of reducing the burden of urogenital tract infections in an antibiotic-sparing manner.
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Affiliation(s)
- Kevin O Tamadonfar
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Natalie S Omattage
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
| | - Caitlin N Spaulding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Harvard University School of Public Health, Boston, MA 02115
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University, School of Medicine, St. Louis, MO 63110
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30
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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: 5] [Impact Index Per Article: 0.8] [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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31
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Merino I, Hernández-García M, Turrientes MC, Pérez-Viso B, López-Fresneña N, Diaz-Agero C, Maechler F, Fankhauser-Rodriguez C, Kola A, Schrenzel J, Harbarth S, Bonten M, Gastmeier P, Canton R, Ruiz-Garbajosa P, Desilets M, Dul S, Scherrer-Muller F, Huttner B, Uçkay I, Prendki V, Renzi G. Emergence of ESBL-producing Escherichia coli ST131-C1-M27 clade colonizing patients in Europe. J Antimicrob Chemother 2018; 73:2973-2980. [DOI: 10.1093/jac/dky296] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/26/2018] [Indexed: 01/12/2023] Open
Affiliation(s)
- Irene Merino
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Hernández-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - María-Carmen Turrientes
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Blanca Pérez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Nieves López-Fresneña
- Servicio de Medicina Preventiva, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Cristina Diaz-Agero
- Servicio de Medicina Preventiva, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Friederike Maechler
- Charité University Medicine, Institute of Hygiene and Environmental Medicine, Hindenburgdamm 27, Berlin, Germany
| | | | - Axel Kola
- Charité University Medicine, Institute of Hygiene and Environmental Medicine, Hindenburgdamm 27, Berlin, Germany
| | - Jacques Schrenzel
- Infection Control Program and Genomic Research Laboratory, University of Geneva Hospitals, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Program and Genomic Research Laboratory, University of Geneva Hospitals, Geneva, Switzerland
| | - Marc Bonten
- Universitair Medisch Centrum Utrecht, Utrecht, The Netherlands
| | - Petra Gastmeier
- Charité University Medicine, Institute of Hygiene and Environmental Medicine, Hindenburgdamm 27, Berlin, Germany
| | - R Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - P Ruiz-Garbajosa
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
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Responses of the Human Gut Escherichia coli Population to Pathogen and Antibiotic Disturbances. mSystems 2018; 3:mSystems00047-18. [PMID: 30057943 PMCID: PMC6060285 DOI: 10.1128/msystems.00047-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/06/2018] [Indexed: 11/23/2022] Open
Abstract
Research on human-associated E. coli tends to focus on pathogens, such as enterotoxigenic E. coli (ETEC) strains, which are a leading cause of diarrhea in developing countries. However, the severity of disease caused by these pathogens is thought to be influenced by the microbiome. The nonpathogenic E. coli community that resides in the human gastrointestinal tract may play a role in pathogen colonization and disease severity and may become a reservoir for virulence and antibiotic resistance genes. Our study used whole-genome sequencing of E. coli before, during, and after challenge with an archetype ETEC isolate, H10407, and antibiotic treatment to explore the diversity and resiliency of the resident E. coli population in response to the ecological disturbances caused by pathogen invasion and antibiotic treatment. Studies of Escherichia coli in the human gastrointestinal tract have focused on pathogens, such as diarrhea-causing enterotoxigenic E. coli (ETEC), while overlooking the resident, nonpathogenic E. coli community. Relatively few genomes of nonpathogenic E. coli strains are available for comparative genomic analysis, and the ecology of these strains is poorly understood. This study examined the diversity and dynamics of resident human gastrointestinal E. coli communities in the face of the ecological challenges presented by pathogen (ETEC) challenge, as well as of antibiotic treatment. Whole-genome sequences obtained from E. coli isolates from before, during, and after ETEC challenge were used in phylogenomic and comparative genomic analyses to examine the diversity of the resident E. coli communities, as well as the dynamics of the challenge strain, H10407, a well-studied ETEC strain (serotype O78:H11) that produces both heat-labile and heat-stable enterotoxins. ETEC failed to become the dominant E. coli clone in two of the six challenge subjects, each of whom exhibited limited or no clinical presentation of diarrhea. The E. coli communities of the remaining four subjects became ETEC dominant during the challenge but reverted to their original, subject-specific populations following antibiotic treatment, suggesting resiliency of the resident E. coli population following major ecological disruptions. This resiliency is likely due in part to the abundance of antibiotic-resistant ST131 E. coli strains in the resident populations. This report provides valuable insights into the potential interactions of members of the gastrointestinal microbiome and its responses to challenge by an external pathogen and by antibiotic exposure. IMPORTANCE Research on human-associated E. coli tends to focus on pathogens, such as enterotoxigenic E. coli (ETEC) strains, which are a leading cause of diarrhea in developing countries. However, the severity of disease caused by these pathogens is thought to be influenced by the microbiome. The nonpathogenic E. coli community that resides in the human gastrointestinal tract may play a role in pathogen colonization and disease severity and may become a reservoir for virulence and antibiotic resistance genes. Our study used whole-genome sequencing of E. coli before, during, and after challenge with an archetype ETEC isolate, H10407, and antibiotic treatment to explore the diversity and resiliency of the resident E. coli population in response to the ecological disturbances caused by pathogen invasion and antibiotic treatment.
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