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Sidorczuk K, Burdukiewicz M, Cerk K, Fritscher J, Kingsley RA, Schierack P, Hildebrand F, Kolenda R. adhesiomeR: a tool for Escherichia coli adhesin classification and analysis. BMC Genomics 2024; 25:609. [PMID: 38886681 PMCID: PMC11184843 DOI: 10.1186/s12864-024-10525-6] [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: 03/10/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
Adhesins are crucial factors in the virulence of bacterial pathogens such as Escherichia coli. However, to date no resources have been dedicated to the detailed analysis of E. coli adhesins. Here, we provide adhesiomeR software that enables characterization of the complete adhesin repertoire, termed the adhesiome. AdhesiomeR incorporates the most comprehensive database of E. coli adhesins and facilitates an extensive analysis of adhesiome. We demonstrate that adhesiomeR achieves 98% accuracy when compared with experimental analyses. Based on analysis of 15,000 E. coli genomes, we define novel adhesiome profiles and clusters, providing a nomenclature for a unified comparison of E. coli adhesiomes.
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Affiliation(s)
- Katarzyna Sidorczuk
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Michał Burdukiewicz
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Cerdanyola del Vallès, Spain
| | - Klara Cerk
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Joachim Fritscher
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Depertment of Biological Sciences, University of East Anglia, Norwich, UK
| | - Peter Schierack
- Institute for Biotechnology, Brandenburg University of Technology (BTU) Cottbus-Senftenberg, Senftenberg, Germany
| | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Earlham Institute, Norwich Research Park, Norwich, UK.
| | - Rafał Kolenda
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland.
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Xing Y, Clark JR, Chang JD, Chirman DM, Green S, Zulk JJ, Jelinski J, Patras KA, Maresso AW. Broad protective vaccination against systemic Escherichia coli with autotransporter antigens. PLoS Pathog 2023; 19:e1011082. [PMID: 36800400 PMCID: PMC9937491 DOI: 10.1371/journal.ppat.1011082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/26/2022] [Indexed: 02/18/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of adult life-threatening sepsis and urinary tract infections (UTI). The emergence and spread of multidrug-resistant (MDR) ExPEC strains result in a considerable amount of treatment failure and hospitalization costs, and contribute to the spread of drug resistance amongst the human microbiome. Thus, an effective vaccine against ExPEC would reduce morbidity and mortality and possibly decrease carriage in healthy or diseased populations. A comparative genomic analysis demonstrated a gene encoding an invasin-like protein, termed sinH, annotated as an autotransporter protein, shows high prevalence in various invasive ExPEC phylogroups, especially those associated with systemic bacteremia and UTI. Here, we evaluated the protective efficacy and immunogenicity of a recombinant SinH-based vaccine consisting of either domain-3 or domains-1,2, and 3 of the putative extracellular region of surface-localized SinH. Immunization of a murine host with SinH-based antigens elicited significant protection against various strains of the pandemic ExPEC sequence type 131 (ST131) as well as multiple sequence types in two distinct models of infection (colonization and bacteremia). SinH immunization also provided significant protection against ExPEC colonization in the bladder in an acute UTI model. Immunized cohorts produced significantly higher levels of vaccine-specific serum IgG and urinary IgG and IgA, findings consistent with mucosal protection. Collectively, these results demonstrate that autotransporter antigens such as SinH may constitute promising ExPEC phylogroup-specific and sequence-type effective vaccine targets that reduce E. coli colonization and virulence.
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Affiliation(s)
- Yikun Xing
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Justin R. Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - James D. Chang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Dylan M. Chirman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sabrina Green
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jacob J. Zulk
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph Jelinski
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kathryn A. Patras
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anthony W. Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
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Zhang F, Meng Y, Xu L, Tian Y, Lu H, Xie J, Ma R, Li M, Li B. KbvR mutant of Klebsiella pneumoniae affects the synthesis of type 1 fimbriae and provides protection to mice as a live attenuated vaccine. Vet Res 2022; 53:97. [DOI: 10.1186/s13567-022-01116-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022] Open
Abstract
AbstractKlebsiella pneumoniae is a leading cause of severe infections in humans and animals, and the emergence of multidrug-resistant strains highlights the need to develop effective vaccines for preventing such infections. Live attenuated vaccines are attractive vaccine candidates available in the veterinary field. We recently characterized that the K. pneumoniae kbvR (Klebsiella biofilm and virulence regulator) mutant was a highly attenuated strain in the mice model. In the present study, the characterization, safety, and protective efficacy of ΔkbvR strain as a live attenuated vaccine were evaluated. The synthesis and activity of type 1 fimbriae were increased in the ΔkbvR strain. All mice inoculated by the subcutaneous route with 105, 106, and 107 colony-forming units (CFU) doses of the ΔkbvR strain survived. Subcutaneous immunization with two doses of 105 or 107 CFU ΔkbvR elicited a robust humoral immune response, and provided protection against the following K. pneumoniae intraperitoneal infection. The antisera of mice immunized with 105 CFU dose improved the opsonophagocytic ability and complement-mediated lysis not only to the same serotype strain but also to the different serotype strain. The passive transfer of antisera from 105 CFU dose-immunized mice provided protection against K. pneumoniae infection. Overall, our results suggest the great potential of the ΔkbvR strain as a novel vaccine candidate against K. pneumoniae infections in herds or humans.
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Montes-Robledo A, Baldiris-Avila R, Galindo JF. D-Mannoside FimH Inhibitors as Non-Antibiotic Alternatives for Uropathogenic Escherichia coli. Antibiotics (Basel) 2021; 10:antibiotics10091072. [PMID: 34572654 PMCID: PMC8465801 DOI: 10.3390/antibiotics10091072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022] Open
Abstract
FimH is a type I fimbria of uropathogenic Escherichia coli (UPEC), recognized for its ability to adhere and infect epithelial urinary tissue. Due to its role in the virulence of UPEC, several therapeutic strategies have focused on the study of FimH, including vaccines, mannosides, and molecules that inhibit their assembly. This work has focused on the ability of a set of monosubstituted and disubstituted phenyl mannosides to inhibit FimH. To determine the 3D structure of FimH for our in silico studies, we obtained fifteen sequences by PCR amplification of the fimH gene from 102 UPEC isolates. The fimH sequences in BLAST had a high homology (97–100%) to our UPEC fimH sequences. A search for the three-dimensional crystallographic structure of FimH proteins in the PDB server showed that proteins 4X5P and 4XO9 were found in 10 of the 15 isolates, presenting a 67% influx among our UPEC isolates. We focused on these two proteins to study the stability, free energy, and the interactions with different mannoside ligands. We found that the interactions with the residues of aspartic acid (ASP 54) and glutamine (GLN 133) were significant to the binding stability. The ligands assessed demonstrated high binding affinity and stability with the lectin domain of FimH proteins during the molecular dynamic simulations, based on MM-PBSA analysis. Therefore, our results suggest the potential utility of phenyl mannoside derivatives as FimH inhibitors to mitigate urinary tract infections produced by UPEC; thus, decreasing colonization, disease burden, and the costs of medical care.
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Affiliation(s)
- Alfredo Montes-Robledo
- Grupo de Investigación Microbiología Clínica y Ambiental, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena de Indias 13001, Colombia;
- Maestría en Microbiología, Facultad de Medicina, Universidad de Cartagena, Cartagena de Indias 13001, Colombia
| | - Rosa Baldiris-Avila
- Grupo de Investigación Microbiología Clínica y Ambiental, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena de Indias 13001, Colombia;
- Maestría en Microbiología, Facultad de Medicina, Universidad de Cartagena, Cartagena de Indias 13001, Colombia
- Grupo de Investigación CIPTEC, Facultad de Ingeniería, Fundacion Universitaria Tecnologico Comfenalco—Cartagena, Cartagena de Indias 13001, Colombia
- Correspondence: (R.B.-A.); (J.F.G.)
| | - Johan Fabian Galindo
- Departamento de Química, Universidad Nacional de Colombia, Bogotá 11321, Colombia
- Correspondence: (R.B.-A.); (J.F.G.)
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Micoli F, Bagnoli F, Rappuoli R, Serruto D. The role of vaccines in combatting antimicrobial resistance. Nat Rev Microbiol 2021; 19:287-302. [PMID: 33542518 PMCID: PMC7861009 DOI: 10.1038/s41579-020-00506-3] [Citation(s) in RCA: 188] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2020] [Indexed: 01/29/2023]
Abstract
The use of antibiotics has enabled the successful treatment of bacterial infections, saving the lives and improving the health of many patients worldwide. However, the emergence and spread of antimicrobial resistance (AMR) has been highlighted as a global threat by different health organizations, and pathogens resistant to antimicrobials cause substantial morbidity and death. As resistance to multiple drugs increases, novel and effective therapies as well as prevention strategies are needed. In this Review, we discuss evidence that vaccines can have a major role in fighting AMR. Vaccines are used prophylactically, decreasing the number of infectious disease cases, and thus antibiotic use and the emergence and spread of AMR. We also describe the current state of development of vaccines against resistant bacterial pathogens that cause a substantial disease burden both in high-income countries and in low- and medium-income countries, discuss possible obstacles that hinder progress in vaccine development and speculate on the impact of next-generation vaccines against bacterial infectious diseases on AMR.
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Affiliation(s)
- Francesca Micoli
- grid.425088.3GSK Vaccines Institute for Global Health, Siena, Italy
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Eldridge GR, Hughey H, Rosenberger L, Martin SM, Shapiro AM, D'Antonio E, Krejci KG, Shore N, Peterson J, Lukes AS, Starks CM. Safety and immunogenicity of an adjuvanted Escherichia coli adhesin vaccine in healthy women with and without histories of recurrent urinary tract infections: results from a first-in-human phase 1 study. Hum Vaccin Immunother 2020; 17:1262-1270. [PMID: 33325785 PMCID: PMC8078672 DOI: 10.1080/21645515.2020.1834807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Antibiotic resistance among gram-negative bacteria continues to rise globally at an alarming rate. New vaccines that prevent bacterial infections and reduce antibiotic use could provide a potential solution to these problems. This study focused on development of an investigational vaccine to prevent recurrent urinary traction infections (UTI) caused by gram-negative bacteria that use type 1 pili to adhere to, invade, and colonize human bladders. The vaccine antigen is FimH, an adhesin protein on the tip of type 1 pili with a lectin binding domain that enables attachment to glycoproteins on mammalian bladders. This was a phase 1, open-label, dose escalation study evaluating the vaccine in 67 healthy women with and without histories of recurrent UTI. The objectives of the study were to evaluate the safety, tolerability, and immunogenicity of different dosages of the antigen and adjuvant of the vaccine. All dosages were well-tolerated and a low incidence of systemic reactions occurred. No serious adverse events related to the vaccine were reported. The vaccine induced both binding and functional antibodies. The women with histories of recurrent UTI demonstrated greater than 150-fold increases in antibodies against the N-terminal region of FimH. Based on the results of this phase 1 study, this vaccine is proceeding to a double-blind, randomized, placebo-controlled phase 2 study. If this vaccine is successful in future studies, it could potentially prevent millions of recurrent UTI globally and reduce the development of antibiotic resistance.
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Affiliation(s)
| | | | - Lois Rosenberger
- LBR Regulatory and Clinical Consulting Services, Inc, Florence, KY, USA
| | | | | | | | | | - Neal Shore
- Atlantic Urology Clinics, Myrtle Beach, SC, USA
| | | | - Andrea S Lukes
- Women's Wellness Clinic, Carolina Women's Research and Wellness Center (CWRWC), Durham, NC, USA
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