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Sada TS, Tessema TS. Isolation and characterization of lytic bacteriophages from various sources in Addis Ababa against antimicrobial-resistant diarrheagenic Escherichia coli strains and evaluation of their therapeutic potential. BMC Infect Dis 2024; 24:310. [PMID: 38486152 PMCID: PMC10938718 DOI: 10.1186/s12879-024-09152-z] [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: 11/23/2023] [Accepted: 02/19/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Escherichia coli is a common fecal coliform, facultative aerobic, gram-negative bacterium. Pathogenic strains of such microbes have evolved to cause diarrhea, urinary tract infections, and septicemias. The emergence of antibiotic resistance urged the identification of an alternative strategy. The use of lytic bacteriophages against the control of pathogenic E. coli in clinics and different environmental setups (waste and drink water management) has become an alternative therapy to antibiotic therapy. Thus, this study aimed to isolate and characterize lytic bacteriophage from various sources in Addis Ababa, tested them against antimicrobial-resistant diarrheagenic E. coli strains and evaluated their therapeutic potential under in vitro conditions. METHODS A total of 14 samples were processed against six different diarrheagenic E. coli strains. The conventional culture and plaque analysis agar overlay method was used to recover lytic bacteriophage isolates. The phage isolates were characterized to determine their lytic effect, growth characteristics, host range activity, and stability under different temperature and pH conditions. Phage isolates were identified by scanning electron microscope (SEM), and molecular techniques (PCR). RESULTS In total, 17 phages were recovered from 84 tested plates. Of the 17 phage isolates, 11 (65%) were Myoviridae-like phages, and 6 (35%) phage isolates were Podoviridae and Siphoviridae by morphology and PCR identification. Based on the host range test, growth characteristics, and stability test 7 potent phages were selected. These phages demonstrated better growth characteristics, including short latent periods, highest burst sizes, and wider host ranges, as well as thermal stability and the ability to survive in a wide range of pH levels. CONCLUSIONS The promising effect of the phages isolated in this study against AMR pathogenic E. coli has raised the possibility of their use in the future treatment of E. coli infections.
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Affiliation(s)
- Tamirat Salile Sada
- Institute of Biotechnology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia.
- Department of Biotechnology, Woldia University, P.O. Box 400, Woldia, Ethiopia.
| | - Tesfaye Sisay Tessema
- Institute of Biotechnology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
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2
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Paroni M, Leccese G, Ranzani V, Moschetti G, Chiara M, Perillo F, Ferri S, Clemente F, Noviello D, Conforti FS, Ferrero S, Karnani B, Bosotti R, Vasco C, Curti S, Crosti MC, Gruarin P, Rossetti G, Conte MP, Vecchi M, Pagani M, Landini P, Facciotti F, Abrignani S, Caprioli F, Geginat J. An Intestinal Th17 Subset is Associated with Inflammation in Crohn's Disease and Activated by Adherent-invasive Escherichia coli. J Crohns Colitis 2023; 17:1988-2001. [PMID: 37462681 PMCID: PMC10798865 DOI: 10.1093/ecco-jcc/jjad119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
IFNγ-producing ex-Th17 cells ['Th1/17'] were shown to play a key pathogenic role in experimental colitis and are abundant in the intestine. Here, we identified and characterised a novel, potentially colitogenic subset of Th17 cells in the intestine of patients with Crohn's disease [CD]. Human Th17 cells expressing CCR5 ['pTh17'] co-expressed T-bet and RORC/γt and produced very high levels of IL-17, together with IFN-γ. They had a gene signature of Th17 effector cells and were distinct from established Th1/17 cells. pTh17 cells, but not Th1/17 cells, were associated with intestinal inflammation in CD, and decreased upon successful anti-TNF therapy with infliximab. Conventional CCR5[-]Th17 cells differentiated to pTh17 cells with IL-23 in vitro. Moreover, anti-IL-23 therapy with risankizumab strongly reduced pTh17 cells in the intestine. Importantly, intestinal pTh17 cells were selectively activated by adherent-invasive Escherichia coli [AIEC], but not by a commensal/probiotic E. coli strain. AIEC induced high levels of IL-23 and RANTES from dendritic cells [DC]. Intestinal CCR5+Th1/17 cells responded instead to cytomegalovirus and were reduced in ulcerative colitis [UC], suggesting an unexpected protective role. In conclusion, we identified an IL-23-inducible subset of human intestinal Th17 cells. pTh17 cells produced high levels of pro-inflammatory cytokines, were selectively associated with intestinal inflammation in CD, and responded to CD-associated AIEC, suggesting a key colitogenic role.
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Affiliation(s)
- Moira Paroni
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Gabriella Leccese
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Valeria Ranzani
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Giorgia Moschetti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Matteo Chiara
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Federica Perillo
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Sara Ferri
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
| | - Francesca Clemente
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Daniele Noviello
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Francesco Simone Conforti
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Ferrero
- Pathology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Biomedical, Surgical, and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Bhavna Karnani
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Roberto Bosotti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Chiara Vasco
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Serena Curti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Maria Cristina Crosti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Paola Gruarin
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Grazisa Rossetti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Molecular Oncology and Immunology, FIRC Institute of Molecular Oncology [IFOM], Milan, Italy
| | - Maria Pia Conte
- Department of Public Health and Infectious Diseases, ‘Sapienza’ University of Rome, Rome, Italy
| | - Maurizio Vecchi
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Massimiliano Pagani
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Molecular Oncology and Immunology, FIRC Institute of Molecular Oncology [IFOM], Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Paolo Landini
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Federica Facciotti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
| | - Sergio Abrignani
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- DISCCO, Department of Clinical Science and Community Health, University of Milan, Milan, Italy
| | - Flavio Caprioli
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Jens Geginat
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- DISCCO, Department of Clinical Science and Community Health, University of Milan, Milan, Italy
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3
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Bleich RM, Li C, Sun S, Ahn JH, Dogan B, Barlogio CJ, Broberg CA, Franks AR, Bulik-Sullivan E, Carroll IM, Simpson KW, Fodor AA, Arthur JC. A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice. MICROBIOME 2023; 11:277. [PMID: 38124090 PMCID: PMC10731797 DOI: 10.1186/s40168-023-01710-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/26/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in vitro definition fully predicts mucosal colonization in vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis. RESULTS Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortium of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization. CONCLUSIONS Our findings establish the in vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in vivo colonization dynamics of patient-derived bacteria in murine models. Video Abstract.
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Affiliation(s)
- Rachel M Bleich
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biology, Appalachian State University, Boone, NC, USA
| | - Chuang Li
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shan Sun
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Ju-Hyun Ahn
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Belgin Dogan
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Cassandra J Barlogio
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher A Broberg
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adrienne R Franks
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily Bulik-Sullivan
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ian M Carroll
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth W Simpson
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Anthony A Fodor
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Janelle C Arthur
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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4
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Flores E, Dutta S, Bosserman R, van Hoof A, Krachler AM. Colonization of larval zebrafish ( Danio rerio) with adherent-invasive Escherichia coli prevents recovery of the intestinal mucosa from drug-induced enterocolitis. mSphere 2023; 8:e0051223. [PMID: 37971273 PMCID: PMC10732064 DOI: 10.1128/msphere.00512-23] [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: 09/05/2023] [Accepted: 10/07/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Although inflammatory bowel diseases are on the rise, what factors influence IBD risk and severity, and the underlying mechanisms remain to be fully understood. Although host genetics, microbiome, and environmental factors have all been shown to correlate with the development of IBD, cause and effect are difficult to disentangle in this context. For example, AIEC is a known pathobiont found in IBD patients, but it remains unclear if gut inflammation during IBD facilitates colonization with AIEC, or if AIEC colonization makes the host more susceptible to pro-inflammatory stimuli. It is critical to understand the mechanisms that contribute to AIEC infections in a susceptible host in order to develop successful therapeutics. Here, we show that the larval zebrafish model recapitulates key features of AIEC infections in other animal models and can be utilized to address these gaps in knowledge.
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Affiliation(s)
- Erika Flores
- Microbiology and Infectious Diseases Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Soumita Dutta
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Rachel Bosserman
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ambro van Hoof
- Microbiology and Infectious Diseases Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Anne-Marie Krachler
- Microbiology and Infectious Diseases Program, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, Texas, USA
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
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5
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Bertin B, Foligne B, Ley D, Lesage J, Beghin L, Morcel J, Gottrand F, Hermann E. An Overview of the Influence of Breastfeeding on the Development of Inflammatory Bowel Disease. Nutrients 2023; 15:5103. [PMID: 38140362 PMCID: PMC10745409 DOI: 10.3390/nu15245103] [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: 11/22/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
The first 1000 days of life is a critical period that contributes significantly to the programming of an individual's future health. Among the many changes that occur during this period early in life, there is growing evidence that the establishment of healthy gut microbiota plays an important role in the prevention of both short- and long-term health problems. Numerous publications suggest that the quality of the gut microbiota colonisation depends on several dietary factors, including breastfeeding. In this respect, a relationship between breastfeeding and the risk of inflammatory bowel disease (IBD) has been suggested. IBDs are chronic intestinal diseases, and perinatal factors may be partly responsible for their onset. We review the existence of links between breastfeeding and IBD based on experimental and clinical studies. Overall, despite encouraging experimental data in rodents, the association between breastfeeding and the development of IBD remains controversial in humans, partly due to the considerable heterogeneity between clinical studies. The duration of exclusive breastfeeding is probably decisive for its lasting effect on IBD. Thus, specific improvements in our knowledge could support dietary interventions targeting the gut microbiome, such as the early use of prebiotics, probiotics or postbiotics, in order to prevent the disease.
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Affiliation(s)
- Benjamin Bertin
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France; (B.B.); (B.F.); (D.L.); (J.L.); (L.B.); (J.M.); (F.G.)
| | - Benoit Foligne
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France; (B.B.); (B.F.); (D.L.); (J.L.); (L.B.); (J.M.); (F.G.)
| | - Delphine Ley
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France; (B.B.); (B.F.); (D.L.); (J.L.); (L.B.); (J.M.); (F.G.)
| | - Jean Lesage
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France; (B.B.); (B.F.); (D.L.); (J.L.); (L.B.); (J.M.); (F.G.)
| | - Laurent Beghin
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France; (B.B.); (B.F.); (D.L.); (J.L.); (L.B.); (J.M.); (F.G.)
- Univ. Lille, Inserm, CHU Lille, CIC-1403 Inserm-CHU, F-59000 Lille, France
| | - Jules Morcel
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France; (B.B.); (B.F.); (D.L.); (J.L.); (L.B.); (J.M.); (F.G.)
- Univ. Lille, Inserm, CHU Lille, CIC-1403 Inserm-CHU, F-59000 Lille, France
| | - Frédéric Gottrand
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France; (B.B.); (B.F.); (D.L.); (J.L.); (L.B.); (J.M.); (F.G.)
- Univ. Lille, Inserm, CHU Lille, CIC-1403 Inserm-CHU, F-59000 Lille, France
| | - Emmanuel Hermann
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, F-59000 Lille, France; (B.B.); (B.F.); (D.L.); (J.L.); (L.B.); (J.M.); (F.G.)
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Bleich RM, Li C, Sun S, Barlogio CJ, Broberg CA, Franks AR, Bulik-Sullivan E, Dogan B, Simpson KW, Carroll IM, Fodor AA, Arthur JC. A consortia of clinical E. coli strains with distinct in-vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice. RESEARCH SQUARE 2023:rs.3.rs-2899665. [PMID: 37214858 PMCID: PMC10197778 DOI: 10.21203/rs.3.rs-2899665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in-vitro definition fully predicts mucosal colonization in-vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis. Results Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortia of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization. Conclusions Our findings establish the in-vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in-vivo colonization dynamics of patient-derived bacteria in murine models.
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Affiliation(s)
| | - Chuang Li
- University of North Carolina at Chapel Hill
| | - Shan Sun
- University of North Carolina at Charlotte
| | | | | | | | | | - Belgin Dogan
- Cornell University College of Veterinary Medicine
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7
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Evidence for a Causal Role for Escherichia coli Strains Identified as Adherent-Invasive (AIEC) in Intestinal Inflammation. mSphere 2023; 8:e0047822. [PMID: 36883813 PMCID: PMC10117065 DOI: 10.1128/msphere.00478-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Enrichment of adherent-invasive Escherichia coli (AIEC) has been consistently detected in subsets of inflammatory bowel disease (IBD) patients. Although some AIEC strains cause colitis in animal models, these studies did not systematically compare AIEC with non-AIEC strains, and causal links between AIEC and disease are still disputed. Specifically, it remains unclear whether AIEC shows enhanced pathogenicity compared to that of commensal E. coli found in the same ecological microhabitat and if the in vitro phenotypes used to classify strains as AIEC are pathologically relevant. Here, we utilized in vitro phenotyping and a murine model of intestinal inflammation to systematically compare strains identified as AIEC with those identified as non-AIEC and relate AIEC phenotypes to pathogenicity. Strains identified as AIEC caused, on average, more severe intestinal inflammation. Intracellular survival/replication phenotypes routinely used to classify AIEC positively correlated with disease, while adherence to epithelial cells and tumor necrosis factor alpha production by macrophages did not. This knowledge was then applied to design and test a strategy to prevent inflammation by selecting E. coli strains that adhered to epithelial cells but poorly survived/replicated intracellularly. Two E. coli strains that ameliorated AIEC-mediated disease were subsequently identified. In summary, our results show a relationship between intracellular survival/replication in E. coli and pathology in murine colitis, suggesting that strains possessing these phenotypes might not only become enriched in human IBD but also contribute to disease. We provide new evidence that specific AIEC phenotypes are pathologically relevant and proof of principle that such mechanistic information can be therapeutically exploited to alleviate intestinal inflammation. IMPORTANCE Inflammatory bowel disease (IBD) is associated with an altered gut microbiota composition, including expansion of Proteobacteria. Many species in this phylum are thought to contribute to disease under certain conditions, including adherent-invasive Escherichia coli (AIEC) strains, which are enriched in some patients. However, whether this bloom contributes to disease or is just a response to IBD-associated physiological changes is unknown. Although assigning causality is challenging, appropriate animal models can test the hypothesis that AIEC strains have an enhanced ability to cause colitis in comparison to other gut commensal E. coli strains and to identify bacterial traits contributing to virulence. We observed that AIEC strains are generally more pathogenic than commensal E. coli and that bacterial intracellular survival/replication phenotypes contributed to disease. We also found that E. coli strains lacking primary virulence traits can prevent inflammation. Our findings provide critical information on E. coli pathogenicity that may inform development of IBD diagnostic tools and therapies.
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Pokharel P, Dhakal S, Dozois CM. The Diversity of Escherichia coli Pathotypes and Vaccination Strategies against This Versatile Bacterial Pathogen. Microorganisms 2023; 11:344. [PMID: 36838308 PMCID: PMC9965155 DOI: 10.3390/microorganisms11020344] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Escherichia coli (E. coli) is a gram-negative bacillus and resident of the normal intestinal microbiota. However, some E. coli strains can cause diseases in humans, other mammals and birds ranging from intestinal infections, for example, diarrhea and dysentery, to extraintestinal infections, such as urinary tract infections, respiratory tract infections, meningitis, and sepsis. In terms of morbidity and mortality, pathogenic E. coli has a great impact on public health, with an economic cost of several billion dollars annually worldwide. Antibiotics are not usually used as first-line treatment for diarrheal illness caused by E. coli and in the case of bloody diarrhea, antibiotics are avoided due to the increased risk of hemolytic uremic syndrome. On the other hand, extraintestinal infections are treated with various antibiotics depending on the site of infection and susceptibility testing. Several alarming papers concerning the rising antibiotic resistance rates in E. coli strains have been published. The silent pandemic of multidrug-resistant bacteria including pathogenic E. coli that have become more difficult to treat favored prophylactic approaches such as E. coli vaccines. This review provides an overview of the pathogenesis of different pathotypes of E. coli, the virulence factors involved and updates on the major aspects of vaccine development against different E. coli pathotypes.
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Affiliation(s)
- Pravil Pokharel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Sabin Dhakal
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Charles M. Dozois
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Faculté de Médecine Vétérinaire, Université de Montréal Saint-Hyacinthe, Saint-Hyacinthe, QC J2S 2M2, Canada
- Pasteur Network, Laval, QC H7V 1B7, Canada
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Abstract
The surge in inflammatory bowel diseases, like Crohn's disease (CD), is alarming. While the role of the gut microbiome in CD development is unresolved, the frequent isolation of adherent-invasive Escherichia coli (AIEC) strains from patient biopsies, together with their propensity to trigger gut inflammation, underpin the potential role of these bacteria as disease modifiers. In this review, we explore the spectrum of AIEC pathogenesis, including their metabolic versatility in the gut. We describe how AIEC strains hijack the host defense mechanisms to evade immune attrition and promote inflammation. Furthermore, we highlight the key traits that differentiate AIEC from commensal E. coli. Deciphering the main components of AIEC virulence is cardinal to the discovery of the next generation of antimicrobials that can selectively eradicate CD-associated bacteria.
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Affiliation(s)
- Sarah Mansour
- Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Canada
| | - Tahreem Asrar
- Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Canada
| | - Wael Elhenawy
- Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Canada,Division of Gastroenterology, Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada,Li Ka Shing Institute of Virology, Canada,Women and Children’s Health Research Institute, Edmonton, Alberta, Canada,Antimicrobial Resistance, One Health Consortium - Edmonton, AB, Canada,CONTACT Wael Elhenawy Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta
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10
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Dubinsky V, Reshef L, Rabinowitz K, Wasserberg N, Dotan I, Gophna U. Escherichia coli Strains from Patients with Inflammatory Bowel Diseases have Disease-specific Genomic Adaptations. J Crohns Colitis 2022; 16:1584-1597. [PMID: 35560165 DOI: 10.1093/ecco-jcc/jjac071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIMS Escherichia coli is over-abundant in the gut microbiome of patients with inflammatory bowel disease [IBD]. Here, we aimed to identify IBD-specific genomic functions of diverse E. coli lineages. METHODS We investigated E. coli genomes from patients with ulcerative colitis [UC], Crohn's disease [CD] or a pouch, and healthy subjects. The majority of genomes were reconstructed from metagenomic samples, including newly sequenced faecal metagenomes. Clinical metadata were collected. Functional analysis at the gene and mutation level were performed and integrated with IBD phenotypes and biomarkers. RESULTS Overall, 530 E. coli genomes were analysed. The E. coli B2 lineage was more prevalent in UC compared with other IBD phenotypes. Genomic metabolic capacities varied across E. coli lineages and IBD phenotypes. Host mucin utilisation enzymes were present in a single lineage and depleted in patients with a pouch, whereas those involved in inulin hydrolysis were enriched in patients with a pouch. E. coli strains from patients with UC were twice as likely to encode the genotoxic molecule colibactin than strains from patients with CD or a pouch. Strikingly, patients with a pouch showed the highest inferred E. coli growth rates, even in the presence of antibiotics. Faecal calprotectin did not correlate with the relative abundance of E. coli. Finally, we identified multiple IBD-specific non-synonymous mutations in E. coli genes encoding for bacterial cell envelope components. CONCLUSIONS Comparative genomics indicates that E. coli is a commensal species adapted to the overactive mucosal immune milieu in IBD, rather than causing it. Our results reveal mutations that may lead to attenuated antigenicity in some E. coli strains.
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Affiliation(s)
- Vadim Dubinsky
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Leah Reshef
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
| | - Keren Rabinowitz
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Nir Wasserberg
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel.,Colorectal Unit, Division of Surgery, Rabin Medical Center, Petah-Tikva, Israel
| | - Iris Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Uri Gophna
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel Aviv, Israel
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11
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Nag D, Farr D, Raychaudhuri S, Withey JH. An adult zebrafish model for adherent-invasive Escherichia coli indicates protection from AIEC infection by probiotic E. coli Nissle. iScience 2022; 25:104572. [PMID: 35769878 PMCID: PMC9234234 DOI: 10.1016/j.isci.2022.104572] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/02/2022] [Accepted: 06/06/2022] [Indexed: 12/30/2022] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) is an opportunistic pathogen associated with major inflammatory bowel disease, Crohn disease, and ulcerative colitis. Unfavorable conditions push commensal AIEC to induce gut inflammation, sometimes progressing to inflammation-induced colon cancer. Recently, zebrafish have emerged as a useful model to study human intestinal pathogens. Here, a zebrafish model to study AIEC infection was developed. Bath inoculation with AIEC resulted in colonization and tissue disruption in the zebrafish intestine. Gene expression of pro-inflammatory markers including interleukin-1β (IL-1β), tumor necrosis factor alpha (TNFα), interferon-γ (IFNγ), and S100A-10b (akin to human calprotectin) in the zebrafish intestine was significantly induced by AIEC infection. The probiotic E. coli Nissle 1917 (EcN) was tested as a therapeutic and prophylactic against AIEC infection and reduced AIEC colonization, tissue damage, and pro-inflammatory responses in zebrafish. Furthermore, EcN diminished the propionic-acid-augmented hyperinfection of AIEC in zebrafish. Thus, this study shows the efficacy of EcN against AIEC in an AIEC-zebrafish model. AIEC can colonize, invade, and induce inflammation in the zebrafish gut Probiotic E. coli Nissle can protect zebrafish from AIEC infection EcN is effective both prophylactically and therapeutically against AIEC-induced IBD
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Affiliation(s)
- Dhrubajyoti Nag
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Dustin Farr
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Saumya Raychaudhuri
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Jeffrey H. Withey
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
- Corresponding author
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12
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López-Siles M, Camprubí-Font C, Gómez Del Pulgar EM, Sabat Mir M, Busquets D, Sanz Y, Martinez-Medina M. Prevalence, Abundance, and Virulence of Adherent-Invasive Escherichia coli in Ulcerative Colitis, Colorectal Cancer, and Coeliac Disease. Front Immunol 2022; 13:748839. [PMID: 35359974 PMCID: PMC8960851 DOI: 10.3389/fimmu.2022.748839] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/31/2022] [Indexed: 01/08/2023] Open
Abstract
Background & Aims Adherent-invasive E. coli (AIEC) has largely been implicated in the pathogenesis of Crohn’s disease (CD). E. coli strains with similar genetic backgrounds and virulence genes profiles have been associated with other intestinal disorders, such as ulcerative colitis (UC), colorectal cancer (CRC), and coeliac disease (CeD), but the role of AIEC in these diseases remains unexplored. We aimed to assess the distribution, abundance, and pathogenic features of AIEC in UC, CRC, and CeD. Methods The AIEC phenotype was investigated in 4,233 E. coli isolated from the ileum and colon of 14 UC and 15 CRC patients and in 38 fecal E. coli strains obtained from 17 CeD and 10 healthy (H) children. AIEC prevalence and abundance were compared with previous data from CD patients and H controls. Clonality, virulence gene carriage, and phylogenetic origin were determined for the AIEC identified. Results In UC, AIEC prevalence was intermediate between CD and H subjects (UC: 35.7%, CD: 55.0%, H: 21.4%), and similar to CD patients with colonic disease (C-CD: 40.0%). In CRC, the prevalence was lower (6.7%) than these groups. In patients with AIEC, the estimated abundance was similar across all intestinal conditions. All AIEC strains isolated from UC and CRC belonged to the B1 phylogroup, except for a strain of the A phylogroup, and the majority (75% of clonally distinct AIEC) harbored the Afa/Dr operon and the cdt gene. None of the E. coli isolated from the CeD cohort were AIEC. Nonetheless, E. coli strains isolated from active CeD patients showed higher invasion indices than those isolated from H and inactive CeD pediatric patients. Conclusion We support the hypothesis that AIEC-like strains can be involved not only in CD but also in UC. Further works are needed to study the virulence particularities of these groups of strains and to determine if there is a causative link between AIEC and UC. In contrast, we rule out the possible association of AIEC with CRC. In addition, to further study the E. coli strains in CeD for their possible pathogenic role would be of interest.
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Affiliation(s)
- Mireia López-Siles
- Microbiology of Intestinal Diseases, Biology Department, Universitat de Girona, Girona, Spain
| | - Carla Camprubí-Font
- Microbiology of Intestinal Diseases, Biology Department, Universitat de Girona, Girona, Spain
| | - Eva M Gómez Del Pulgar
- Instituto de Agroquímica y Tecnología de Alimentos, Spanish National Research Council (CSIC), Paterna, Spain
| | - Miriam Sabat Mir
- Department of Gastroenterology, Hospital Santa Caterina, Salt, Spain
| | - David Busquets
- Department of Gastroenterology, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Yolanda Sanz
- Instituto de Agroquímica y Tecnología de Alimentos, Spanish National Research Council (CSIC), Paterna, Spain
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13
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Kamali Dolatabadi R, Feizi A, Halaji M, Fazeli H, Adibi P. The Prevalence of Adherent-Invasive Escherichia coli and Its Association With Inflammatory Bowel Diseases: A Systematic Review and Meta-Analysis. Front Med (Lausanne) 2021; 8:730243. [PMID: 34926490 PMCID: PMC8678049 DOI: 10.3389/fmed.2021.730243] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are known as chronic gastrointestinal inflammatory disorders. The present systematic review and meta analysis was conducted to estimate the prevalence of adherent-invasive Escherichia coli (AIEC) isolates and their phylogenetic grouping among IBD patients compared with the controls. A systematic literature search was conducted among published papers by international authors until April 30, 2020 in Web of Science, Scopus, EMBASE, and PubMed databases. The pooled prevalence of AIEC isolates and their phylogenetic grouping among IBD patients as well as in controls was estimated using fixed or random effects models. Furthermore, for estimating the association of colonization by AIEC with IBD, odds ratio along with 95% confidence interval was reported. A total of 205 articles retrieved by the initial search of databases, 13 case–control studies met the eligibility criteria for inclusion in the meta analysis. There were 465 IBD cases (348 CD and 117 UC) and 307 controls. The pooled prevalence of AIEC isolates were 28% (95% CI: 18–39%), 29% (95% CI: 20–40%), 13% (95% CI: 1–30%), and 9% (95% CI: 3–19%), respectively among IBD, CD, UC, and control group, respectively. Our results revealed that the most frequent AIEC phylogroup in the IBD, CD, and control groups was B2. Fixed-effects meta analysis showed that colonization of AIEC is significantly associated with IBD (OR: 2.93; 95% CI: 1.90–4.52; P < 0.001) and CD (OR: 3.07; 95% CI: 1.99–4.74; P < 0.001), but not with UC (OR: 2.29; 95% CI: 0.81–6.51; P = 0.11). In summary, this meta analysis revealed that colonization by AIEC is more frequent in IBD and is associated with IBD (CD and UC). Our results suggested that the affects of IBD in patients colonized with the AIEC pathovar is not random, it is in fact a specific disease-related pathovar.
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Affiliation(s)
- Razie Kamali Dolatabadi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Awat Feizi
- Department of Biostatistics and Epidemiology, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran.,Department of Microbiology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Hossein Fazeli
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Peyman Adibi
- Gastroenterology and Hepatology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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14
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The prevalence of the iutA and ibeA genes in Escherichia coli isolates from severe and non-severe patients with bacteremic acute biliary tract infection is significantly different. Gut Pathog 2021; 13:32. [PMID: 34006312 PMCID: PMC8132388 DOI: 10.1186/s13099-021-00429-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 05/12/2021] [Indexed: 12/17/2022] Open
Abstract
Background Although Escherichia coli is the most frequently isolated microorganism in acute biliary tract infections with bacteremia, data regarding its virulence are limited. Results Information on cases of bacteremia in acute biliary tract infection in a retrospective study was collected from 2013 to 2015 at a tertiary care hospital in Japan. Factors related to the severity of infection were investigated, including patient background, phylogenetic typing, and virulence factors of E. coli, such as adhesion, invasion, toxins, and iron acquisition. In total, 72 E. coli strains were identified in 71 cases, most of which primarily belonged to the B2 phylogroup (68.1%). The presence of the iutA gene (77.3% in the non-severe group, 46.4% in the severe group, P = 0.011) and the ibeA gene (9.1% in the non-severe group, and 35.7% in the severe group, P = 0.012) was significantly associated with the severity of infection. Among the patient characteristics, diabetes mellitus with organ involvement and alkaline phosphatase were different in the severe and non-severe groups. Conclusions We showed that bacteremic E. coli strains from acute biliary tract infections belonged to the virulent (B2) phylogroup. The prevalence of the iutA and ibeA genes between the two groups of bacteremia severity was significantly different.
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15
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Nadalian B, Yadegar A, Houri H, Olfatifar M, Shahrokh S, Asadzadeh Aghdaei H, Suzuki H, Zali MR. Prevalence of the pathobiont adherent-invasive Escherichia coli and inflammatory bowel disease: a systematic review and meta-analysis. J Gastroenterol Hepatol 2021; 36:852-863. [PMID: 32929762 DOI: 10.1111/jgh.15260] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/08/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIM Escherichia coli pathobionts and particularly the adherent-invasive E. coli (AIEC) may play a putative role in initiating and maintaining the inflammatory process in the intestinal tissues of inflammatory bowel disease (IBD) patients, by providing stimulatory factors that trigger gut immune system activation. The aim of this study is to conduct a systematic review and meta-analysis to determine the prevalence of AIEC among patients with Crohn's disease (CD) and ulcerative colitis (UC). METHODS Electronic databases were searched up to February 2020 for relevant publications reporting the prevalence of AIEC in IBD patients. The prevalence rate of AIEC among CD and UC patients, the odds ratio (OR) and 95% confidence interval (CI) were calculated compared to non-IBD controls. RESULTS The final dataset included 12 studies, all investigating AIEC isolates from ileal/colonic specimens. The OR for prevalence of AIEC in CD patients was 3.27 (95% CI 1.79-5.9) compared with non-IBD controls. The overall pooled prevalence of AIEC among CD patients was 29% (95% CI 0.17-0.45), whereas this prevalence was calculated to be 9% (95% CI 0.03-0.19) in controls. Moreover, the prevalence of AIEC in UC subjects was calculated 12% (95% CI 0.01-0.34), while AIEC showed a prevalence of 5% (95% CI 0.0-0.17) among the controls. The OR for prevalence of AIEC in UC patients was 2.82 (95% CI 1.11-7.14) compared with controls. CONCLUSIONS There is a substantial increase in the prevalence of AIEC in IBD patients compared with controls. This review supports the growing evidence that AIEC could be involved in both CD and UC pathogenesis.
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Affiliation(s)
- Banafsheh Nadalian
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Houri
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Meysam Olfatifar
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hidekazu Suzuki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, School of Medicine, Tokai University, Isehara, Japan
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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16
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Mayorgas A, Dotti I, Martínez-Picola M, Esteller M, Bonet-Rossinyol Q, Ricart E, Salas A, Martínez-Medina M. A Novel Strategy to Study the Invasive Capability of Adherent-Invasive Escherichia coli by Using Human Primary Organoid-Derived Epithelial Monolayers. Front Immunol 2021; 12:646906. [PMID: 33854511 PMCID: PMC8039293 DOI: 10.3389/fimmu.2021.646906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Over the last decades, Adherent-Invasive Escherichia coli (AIEC) has been linked to the pathogenesis of Crohn’s Disease. AIEC’s characteristics, as well as its interaction with the gut immune system and its role in intestinal epithelial barrier dysfunction, have been extensively studied. Nevertheless, the currently available techniques to investigate the cross-talk between this pathogen and intestinal epithelial cells (IECs) are based on the infection of immortalized cell lines. Despite their many advantages, cell lines cannot reproduce the conditions in tissues, nor do they reflect interindividual variability or gut location-specific traits. In that sense, the use of human primary cultures, either healthy or diseased, offers a system that can overcome all of these limitations. Here, we developed a new infection model by using freshly isolated human IECs. For the first time, we generated and infected monolayer cultures derived from human colonic organoids to study the mechanisms and effects of AIEC adherence and invasion on primary human epithelial cells. To establish the optimal conditions for AIEC invasion studies in human primary organoid-derived epithelial monolayers, we designed an infection-kinetics study to assess the infection dynamics at different time points, as well as with two multiplicities of infection (MOI). Overall, this method provides a model for the study of host response to AIEC infections, as well as for the understanding of the molecular mechanisms involved in adhesion, invasion and intracellular replication. Therefore, it represents a promising tool for elucidating the cross-talk between AIEC and the intestinal epithelium in healthy and diseased tissues.
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Affiliation(s)
- Aida Mayorgas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Isabella Dotti
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Marta Martínez-Picola
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Miriam Esteller
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Queralt Bonet-Rossinyol
- Laboratory of Molecular Microbiology, Department of Biology, Universitat de Girona, Girona, Spain
| | - Elena Ricart
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Azucena Salas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
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17
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The Role of Enterobacteriaceae in Gut Microbiota Dysbiosis in Inflammatory Bowel Diseases. Microorganisms 2021; 9:microorganisms9040697. [PMID: 33801755 PMCID: PMC8066304 DOI: 10.3390/microorganisms9040697] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are a group of chronic gastrointestinal inflammatory diseases with unknown etiology. There is a combination of well documented factors in their pathogenesis, including intestinal microbiota dysbiosis. The symbiotic microbiota plays important functions in the host, and the loss of beneficial microbes could favor the expansion of microbial pathobionts. In particular, the bloom of potentially harmful Proteobacteria, especially Enterobacteriaceae, has been described as enhancing the inflammatory response, as observed in IBDs. Herein, we seek to investigate the contribution of Enterobacteriaceae to IBD pathogenesis whilst considering the continuous expansion of the literature and data. Despite the mechanism of their expansion still remaining unclear, their expansion could be correlated with the increase in nitrate and oxygen levels in the inflamed gut and with the bile acid dysmetabolism described in IBD patients. Furthermore, in several Enterobacteriaceae studies conducted at a species level, it has been suggested that some adherent-invasive Escherichia coli (AIEC) play an important role in IBD pathogenesis. Overall, this review highlights the pivotal role played by Enterobacteriaceae in gut dysbiosis associated with IBD pathogenesis and progression.
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18
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Zhou Y, He Y, Liu L, Zhou W, Wang P, Hu H, Nie Y, Chen Y. Alterations in Gut Microbial Communities Across Anatomical Locations in Inflammatory Bowel Diseases. Front Nutr 2021; 8:615064. [PMID: 33718417 PMCID: PMC7952524 DOI: 10.3389/fnut.2021.615064] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
We previously discovered that gut microbiota can serve as universal microbial biomarkers for diagnosis, disease activity assessment, and predicting the response to infliximab treatment for inflammatory bowel diseases (IBD). Much still remains unknown about the relationship between alterations in gut microbiota and IBD affected bowel region, in particular in the case of ulcerative colitis (UC) and colonic Crohn's disease (cCD) without endoscopic and biopsy data. In the current study gut microbiota from a population in China was found to be distinct from that of the Western world [Human Microbiome Project (HMP) data]. Furthermore, both gut microbiota greatly differed from microbiota of other anatomical locations (oral, skin, airway, and vagina), with higher alpha-diversity (Chinese gut > HMP gut > oral microbiome > airway microbiome > skin microbiome > vaginal microbiome), and marked differences in microbiome composition. In patients with IBD in China, UC was characterized by the presence of Gardnerella, while cCD was characterized by the presence of Fusobacterium. Moreover, gut microbiota, such as Gardnerella and Fusobacterium, may be potential biomarkers for identifying UC from cCD. Together, this study revealed crucial differences in microbial communities across anatomical locations, and demonstrated that there was an important association between IBD affected bowel region and gut microbiota.
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Affiliation(s)
- Youlian Zhou
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yan He
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Le Liu
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wanyan Zhou
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Pu Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Han Hu
- Shenzhen Xbiome Biotech Co. Ltd., Shenzhen, China
| | - Yuqiang Nie
- Department of Gastroenterology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Ye Chen
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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19
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Banfi D, Moro E, Bosi A, Bistoletti M, Cerantola S, Crema F, Maggi F, Giron MC, Giaroni C, Baj A. Impact of Microbial Metabolites on Microbiota-Gut-Brain Axis in Inflammatory Bowel Disease. Int J Mol Sci 2021; 22:1623. [PMID: 33562721 PMCID: PMC7915037 DOI: 10.3390/ijms22041623] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
The complex bidirectional communication system existing between the gastrointestinal tract and the brain initially termed the "gut-brain axis" and renamed the "microbiota-gut-brain axis", considering the pivotal role of gut microbiota in sustaining local and systemic homeostasis, has a fundamental role in the pathogenesis of Inflammatory Bowel Disease (IBD). The integration of signals deriving from the host neuronal, immune, and endocrine systems with signals deriving from the microbiota may influence the development of the local inflammatory injury and impacts also more distal brain regions, underlying the psychophysiological vulnerability of IBD patients. Mood disorders and increased response to stress are frequently associated with IBD and may affect the disease recurrence and severity, thus requiring an appropriate therapeutic approach in addition to conventional anti-inflammatory treatments. This review highlights the more recent evidence suggesting that alterations of the microbiota-gut-brain bidirectional communication axis may concur to IBD pathogenesis and sustain the development of both local and CNS symptoms. The participation of the main microbial-derived metabolites, also defined as "postbiotics", such as bile acids, short-chain fatty acids, and tryptophan metabolites in the development of IBD-associated gut and brain dysfunction will be discussed. The last section covers a critical evaluation of the main clinical evidence pointing to the microbiome-based therapeutic approaches for the treatment of IBD-related gastrointestinal and neuropsychiatric symptoms.
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Affiliation(s)
- Davide Banfi
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
| | - Elisabetta Moro
- Department of Internal Medicine and Therapeutics, Section of Pharmacology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (E.M.); (F.C.)
| | - Annalisa Bosi
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
| | - Michela Bistoletti
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
| | - Silvia Cerantola
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Largo Meneghetti 2, 35131 Padova, Italy; (S.C.); (M.C.G.)
| | - Francesca Crema
- Department of Internal Medicine and Therapeutics, Section of Pharmacology, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (E.M.); (F.C.)
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
| | - Maria Cecilia Giron
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Largo Meneghetti 2, 35131 Padova, Italy; (S.C.); (M.C.G.)
| | - Cristina Giaroni
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
- Centre of Neuroscience, University of Insubria, 21100 Varese, Italy
| | - Andreina Baj
- Department of Medicine and Surgery, University of Insubria, via H Dunant 5, 21100 Varese, Italy; (D.B.); (A.B.); (M.B.); (F.M.); (A.B.)
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20
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Cutone A, Ianiro G, Lepanto MS, Rosa L, Valenti P, Bonaccorsi di Patti MC, Musci G. Lactoferrin in the Prevention and Treatment of Intestinal Inflammatory Pathologies Associated with Colorectal Cancer Development. Cancers (Basel) 2020; 12:E3806. [PMID: 33348646 PMCID: PMC7766217 DOI: 10.3390/cancers12123806] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/20/2022] Open
Abstract
The connection between inflammation and cancer is well-established and supported by genetic, pharmacological and epidemiological data. The inflammatory bowel diseases (IBDs), including Crohn's disease and ulcerative colitis, have been described as important promoters for colorectal cancer development. Risk factors include environmental and food-borne mutagens, dysbalance of intestinal microbiome composition and chronic intestinal inflammation, with loss of intestinal epithelial barrier and enhanced cell proliferation rate. Therapies aimed at shutting down mucosal inflammatory response represent the foundation for IBDs treatment. However, when applied for long periods, they can alter the immune system and promote microbiome dysbiosis and carcinogenesis. Therefore, it is imperative to find new safe substances acting as both potent anti-inflammatory and anti-pathogen agents. Lactoferrin (Lf), an iron-binding glycoprotein essential in innate immunity, is generally recognized as safe and used as food supplement due to its multifunctionality. Lf possesses a wide range of immunomodulatory and anti-inflammatory properties against different aseptic and septic inflammatory pathologies, including IBDs. Moreover, Lf exerts anti-adhesive, anti-invasive and anti-survival activities against several microbial pathogens that colonize intestinal mucosa of IBDs patients. This review focuses on those activities of Lf potentially useful for the prevention/treatment of intestinal inflammatory pathologies associated with colorectal cancer development.
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Affiliation(s)
- Antimo Cutone
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy; (A.C.); (G.I.)
| | - Giusi Ianiro
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy; (A.C.); (G.I.)
| | - Maria Stefania Lepanto
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (P.V.)
| | - Luigi Rosa
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (P.V.)
| | - Piera Valenti
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy; (M.S.L.); (L.R.); (P.V.)
| | | | - Giovanni Musci
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy; (A.C.); (G.I.)
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21
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Manchester AC, Dogan B, Guo Y, Simpson KW. Escherichia coli-associated granulomatous colitis in dogs treated according to antimicrobial susceptibility profiling. J Vet Intern Med 2020; 35:150-161. [PMID: 33321554 PMCID: PMC7848323 DOI: 10.1111/jvim.15995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 12/18/2022] Open
Abstract
Background Eradication of intramucosal Escherichia coli correlates with remission of periodic acid‐Schiff‐positive E coli‐associated granulomatous colitis (GC). Treatment failures attributed to multidrug resistant (MDR) bacteria necessitate alternative approaches. Hypothesis/objectives Determine clinical outcome of E coli‐associated GC in dogs treated based on antimicrobial susceptibility profiling and characterize E coli phylogeny and resistance mechanisms. Animals Twenty Boxers and 4 French Bulldogs with E coli‐associated GC. Methods Culture, antimicrobial susceptibility profiling, and molecular characterization of E coli were performed and response to treatment was evaluated. Results Initial biopsy sample culture yielded fluoroquinolone‐sensitive (FQ‐S) E coli from 9/24 dogs and fluoroquinolone‐resistant (FQ‐R) E coli from 15/24. All but 1 FQ‐R E coli were MDR with susceptibility to macrophage‐penetrating antimicrobials restricted to carbapenems in 13/15 dogs. Of 22/24 treated based on susceptibility profiling, 8/9 FQ‐S dogs had complete initial clinical response (CR) during fluoroquinolone (FQ) treatment, whereas 9/13 FQ‐R dogs had complete or partial response (PR) during meropenem or doxycycline treatment. In 5/9 FQ‐S and 12/13 FQ‐R dogs with follow‐up ≥3 months, CR was sustained in 5/5 FQ‐S (median, 25 months; range, 4‐46) whereas 6/12 FQ‐R had long‐term CR (median, 59 months; range 15‐102), 4/12 PR (median, 19 months; range, 5‐65), and 2/12 had no response (NR). Four dogs with long‐term follow‐up died within 4 years of diagnosis, including 2 euthanized for refractory colitis. Escherichia coli were genetically diverse. Fluoroquinolone resistance was associated with mutations in gyrA and parC, with plasmid‐mediated resistance less common. Conclusions and Clinical Importance Antimicrobial treatment guided by susceptibility profiling was associated with positive long‐term outcomes in >80% of cases. Fluoroquinolone‐resistance was widespread and not clonal. Further study is required to optimize treatment for dogs with MDR E coli‐associated GC.
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Affiliation(s)
| | - Belgin Dogan
- Cornell University College of Veterinary Medicine, Ithaca, New York, USA
| | - Yongli Guo
- Cornell University College of Veterinary Medicine, Ithaca, New York, USA
| | - Kenneth W Simpson
- Cornell University College of Veterinary Medicine, Ithaca, New York, USA
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22
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Pobeguts OV, Ladygina VG, Evsyutina DV, Eremeev AV, Zubov AI, Matyushkina DS, Scherbakov PL, Rakitina DV, Fisunov GY. Propionate Induces Virulent Properties of Crohn's Disease-Associated Escherichia coli. Front Microbiol 2020; 11:1460. [PMID: 32733408 PMCID: PMC7360682 DOI: 10.3389/fmicb.2020.01460] [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] [Received: 11/28/2019] [Accepted: 06/04/2020] [Indexed: 12/16/2022] Open
Abstract
Crohn's disease (CD) is a severe chronic immune-mediated granulomatous inflammatory disease of the gastrointestinal tract. The mechanisms of CD pathogenesis remain obscure. Metagenomic analysis of samples from CD patients revealed that several of them have the elevated level of Escherichia coli with adhesive-invasive phenotype (AIEC). Previously, we isolated an E. coli strain CD isolate ZvL2 from a patient with CD, which features AIEC phenotype. Here, we demonstrate that prolonged growth on propionate containing medium stimulates virulent properties of CD isolate ZvL2, while prolonged growth on glucose reduces these properties to levels indistinguishable from laboratory strain K-12 MG1655. Propionate presence also boosts the ability of CD isolate ZvL2 to penetrate and colonize macrophages. The effect of propionate is reversible, re-passaging of CD isolate on M9 medium supplemented with glucose leads to the loss of its virulent properties. Proteome analysis of CD isolate ZvL2 growth in medium supplemented with propionate or glucose revealed that propionate induces expression porins OmpA and OmpW, transcription factors PhoP and OmpR, and universal stress protein UspE, which were previously found to be important for macrophage colonization by enteropathogenic bacteria.
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Affiliation(s)
- Olga V. Pobeguts
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Valentina G. Ladygina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Daria V. Evsyutina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Artem V. Eremeev
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Aleksandr I. Zubov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Daria S. Matyushkina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | | | - Daria V. Rakitina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
| | - Gleb Y. Fisunov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical-Biological Agency, Moscow, Russia
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23
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Study of a classification algorithm for AIEC identification in geographically distinct E. coli strains. Sci Rep 2020; 10:8094. [PMID: 32415168 PMCID: PMC7229014 DOI: 10.1038/s41598-020-64894-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/21/2020] [Indexed: 01/02/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) have been extensively implicated in Crohn’s disease pathogenesis. Currently, AIEC is identified phenotypically, since no molecular marker specific for AIEC exists. An algorithm based on single nucleotide polymorphisms was previously presented as a potential molecular tool to classify AIEC/non-AIEC, with 84% accuracy on a collection of 50 strains isolated in Girona (Spain). Herein, our aim was to determine the accuracy of the tool using AIEC/non-AIEC isolates from different geographical origins and extraintestinal pathogenic E. coli (ExPEC) strains. The accuracy of the tool was significantly reduced (61%) when external AIEC/non-AIEC strains from France, Chile, Mallorca (Spain) and Australia (82 AIEC, 57 non-AIEC and 45 ExPEC strains in total) were included. However, the inclusion of only the ExPEC strains showed that the tool was fairly accurate at differentiating these two close pathotypes (84.6% sensitivity; 79% accuracy). Moreover, the accuracy was still high (81%) for those AIEC/non-AIEC strains isolated from Girona and Mallorca (N = 63); two collections obtained from independent studies but geographically close. Our findings indicate that the presented tool is not universal since it would be only applicable for strains from similar geographic origin and demonstrates the need to include strains from different origins to validate such tools.
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24
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Martinez-Medina M, Strozzi F, Ruiz Del Castillo B, Serrano-Morillas N, Ferrer Bustins N, Martínez-Martínez L. Antimicrobial Resistance Profiles of Adherent Invasive Escherichia coli Show Increased Resistance to β-Lactams. Antibiotics (Basel) 2020; 9:antibiotics9050251. [PMID: 32414140 PMCID: PMC7277491 DOI: 10.3390/antibiotics9050251] [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] [Received: 04/10/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023] Open
Abstract
The adherent invasive Escherichia coli (AIEC) pathotype has been associated with the aetiology of Crohn’s disease (CD). Scarce reports have shown the antimicrobial resistance (AMR) profiles of AIEC. Despite antibiotics not being recommended to treat CD, antimicrobial therapy could be useful in stratified patients, such as AIEC carriers. We examined the antimicrobial resistance profiles of AIEC strains to identify which therapies could be effective or confer a risk for such patients. Phenotypic resistance to 30 antimicrobials was tested according to CLSI standards. AIEC (n = 22) and non-pathogenic E. coli (non-AIEC) strains (n = 37) isolated from the gut mucosa of 31 CD patients and 18 controls were studied. De novo genome sequencing was carried out for 39 of the 59 strains, and AMR genes were searched using the DeepARG database in these genomes and 33 additional AIEC publicly available genomes. The strains isolated from CD and controls showed similar phenotypic AMR profiles. The genomic analysis did not reveal an increased prevalence of AMR genes. However, AIEC strains were more frequently resistant to β-lactams than non-AIEC strains (11 AIEC (50%) and 5 non-AIEC (22%) strains were resistant to at least one β-lactam; p < 0.042). Two AIEC strains were resistant to expanded-spectrum cephalosporins. One strain carried a plasmid-mediated AmpC β-lactamase (CMY-69), and the other presented mutations in the promotor of the intrinsic chromosomal AmpC related to the hyperproduction of this enzyme. The rest of the strains were resistant to β-lactams not including expanded-spectrum cephalosporins. The majority carried TEM-related β-lactamases. Genomic analysis including external AIEC revealed that the gene sul1 encoding for sulphonamide resistance was more frequent in AIEC strains than non-AIEC strains (34.6% vs. 9.5%, p = 0.030). AMR in AIEC is a matter of concern regarding the putative implication of the pathotype in CD. The high proportion of AIEC resistant to β-lactams warrants caution about the risk there may be in the use of these antimicrobials in AIEC-colonized CD patients.
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Affiliation(s)
- Margarita Martinez-Medina
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
- Correspondence: ; Tel.: +34-972-418261
| | - Francesco Strozzi
- Data Science Departement, Enterome Biosciences S.A., 75011 Paris, France;
| | - Belén Ruiz Del Castillo
- Service of Microbiology, Hospital Universitario Marqués de Valdecilla, Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39008 Santander, Spain;
| | - Natalia Serrano-Morillas
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
| | - Nuria Ferrer Bustins
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
| | - Luis Martínez-Martínez
- Unit of Microbiology, University Hospital Reina Sofia, 14004 Córdoba, Spain;
- Maimonides Biomedical Research Institute, 14004 Córdoba, Spain
- Department of Agricultural Chemistry and Microbiology, University of Córdoba, 14004 Córdoba, Spain
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25
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Sevrin G, Massier S, Chassaing B, Agus A, Delmas J, Denizot J, Billard E, Barnich N. Adaptation of adherent-invasive E. coli to gut environment: Impact on flagellum expression and bacterial colonization ability. Gut Microbes 2020; 11:364-380. [PMID: 29494278 PMCID: PMC7524368 DOI: 10.1080/19490976.2017.1421886] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The pathogenesis of Crohn's disease (CD) is multifactorial and involves genetic susceptibility, environmental triggers and intestinal microbiota. Adherent-invasive Escherichia coli (AIEC) are flagellated bacteria more prevalent in CD patients than in healthy subjects and promote chronic intestinal inflammation. We aim at deciphering the role of flagella and flagellin modulation by intestinal conditions. AIEC flagellum expression is required for optimal adhesion to and invasion of intestinal epithelial cells. Interestingly, differential flagellin regulation was observed between commensal E. coli (HS) and AIEC (LF82) strains: flagellum expression by AIEC bacteria, in contrast to that of commensal E. coli, is enhanced under intestinal conditions (the presence of bile acids and mucins). Flagella are involved in the ability of the AIEC LF82 strain to cross a mucus layer in vitro and in vivo, conferring a selective advantage in penetrating the mucus layer and reaching the epithelial surface. In a CEABAC10 mouse model, a non-motile mutant (LF82-ΔfliC) exhibits reduced colonization that is restored by a dextran sodium sulfate treatment that alters mucus layer integrity. Moreover, a mutant that continuously secretes flagellin (LF82-ΔflgM) triggers a stronger inflammatory response than the wild-type strain, and the mutant's ability to colonize the CEABAC10 mouse model is decreased. Overexpression of flagellin in bacteria in contact with epithelial cells can be detrimental to their virulence by inducing acute inflammation that enhances AIEC clearance. AIEC pathobionts must finely modulate flagellum expression during the infection process, taking advantage of their specific virulence gene regulation to improve their adaptability and flexibility within the gut environment.
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Affiliation(s)
- Gwladys Sevrin
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000Clermont-Ferrand, France
| | - Sébastien Massier
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000Clermont-Ferrand, France
| | - Benoit Chassaing
- Neuroscience Institute & Institute for Biomedical Sciences, Georgia State University, Atlanta, USA
| | - Allison Agus
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000Clermont-Ferrand, France
| | - Julien Delmas
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000Clermont-Ferrand, France,Service de Bactériologie, Parasitologie Mycologie, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Jérémy Denizot
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000Clermont-Ferrand, France,Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand, France
| | - Elisabeth Billard
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000Clermont-Ferrand, France,Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand, France
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000Clermont-Ferrand, France,Université Clermont Auvergne, Institut Universitaire de Technologie de Clermont-Ferrand, Clermont-Ferrand, France,CONTACT Nicolas Barnich M2iSH, Inserm, Université Clermont Auvergne, USC-INRA 2018, 28 place Henri Dunant, 63001Clermont-Ferrand, France
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26
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Abdelhalim KA, Uzel A, Gülşen Ünal N. Virulence determinants and genetic diversity of adherent-invasive Escherichia coli (AIEC) strains isolated from patients with Crohn's disease. Microb Pathog 2020; 145:104233. [PMID: 32360521 DOI: 10.1016/j.micpath.2020.104233] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Adherent invasive Escherichia coli (AIEC) are implicated in the pathogenesis of inflammatory bowel diseases (IBD) particularly Crohn's disease (CD). The aim of this study is to isolate, identify, genotype, and characterize the virulence factors and the clinical significance of AIEC strains. METHODS Ileal and colonic biopsies from 24 active CD patients and 15 healthy controls (HC) were collected. E. coli strains were identified by standard biochemical tests and confirmed by MALDI-TOF (bioMerieux, France) system. The AIEC phenotypes were determined by the adhesion, invasion, and survival within macrophages assays. The genetic virulence factors and genotyping characteristics were determined by PCR and PFGE respectively. The abundance and the antibiogram profile of E. coli strains was determined by qPCR and VITEK®2 (bioMerieux, France) automated system respectively. RESULTS E. coli strains from 17 CD patients and 14 HC were isolated, 10 (59%) and 7 (50%) of them were identified as AIEC strains, respectively. We found that chuA and ratA genes were the most significant genetic markers associated with AIEC compared to non-AIEC strains isolated from CD patients and HC p = 0.0119, 0.0094 respectively. The majority of E. coli strains obtained from CD patients showed antibiotic resistance (71%) compared to HC (29%) against at least one antibiotic. The AIEC-like strains were more resistant to antibiotics compared to non-AIEC-like strains (53%) and (21%) respectively. CONCLUSIONS We have determined significant differences between AIEC strains and non-AIEC strains in terms of the prevalence of chuA and ratA virulence genes and the antibiotic resistance profiles. In addition, AIEC strains isolated from CD patients were found to be more resistant to penicillin/beta lactam and aminoglycoside antibiotics than AIEC strains isolated from HC 80%, 14% respectively.
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Affiliation(s)
- Khalid A Abdelhalim
- Ege University, Faculty of Science, Department of Biology, Section of Basic and Industrial Microbiology, Izmir, Turkey
| | - Ataç Uzel
- Ege University, Faculty of Science, Department of Biology, Section of Basic and Industrial Microbiology, Izmir, Turkey
| | - Nalan Gülşen Ünal
- Ege University, Faculty of Medicine, Department of Internal Medicine, Division of Gastroenterology, Izmir, Turkey.
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Camprubí-Font C, Martinez-Medina M. Why the discovery of adherent-invasive Escherichia coli molecular markers is so challenging? World J Biol Chem 2020; 11:1-13. [PMID: 32405343 PMCID: PMC7205867 DOI: 10.4331/wjbc.v11.i1.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/18/2020] [Accepted: 03/31/2020] [Indexed: 02/05/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strains have been extensively related to Crohn’s disease (CD) etiopathogenesis. Higher AIEC prevalence in CD patients versus controls has been reported, and its mechanisms of pathogenicity have been linked to CD physiopathology. In CD, the therapeutic armamentarium remains limited and non-curative; hence, the necessity to better understand AIEC as a putative instigator or propagator of the disease is certain. Nonetheless, AIEC identification is currently challenging because it relies on phenotypic assays based on infected cell cultures which are highly time-consuming, laborious and non-standardizable. To address this issue, AIEC molecular mechanisms and virulence genes have been studied; however, a specific and widely distributed genetic AIEC marker is still missing. The finding of molecular tools to easily identify AIEC could be useful in the identification of AIEC carriers who could profit from personalized treatment. Also, it would significantly promote AIEC epidemiological studies. Here, we reviewed the existing data regarding AIEC genetics and presented those molecular markers that could assist with AIEC identification. Finally, we highlighted the problems behind the discovery of exclusive AIEC biomarkers and proposed strategies to facilitate the search of AIEC signature sequences.
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Affiliation(s)
- Carla Camprubí-Font
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Girona 17003, Spain
| | - Margarita Martinez-Medina
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Girona 17003, Spain
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28
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Enhanced O-linked Glcnacylation in Crohn's disease promotes intestinal inflammation. EBioMedicine 2020; 53:102693. [PMID: 32114385 PMCID: PMC7047186 DOI: 10.1016/j.ebiom.2020.102693] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
Background Treatment of Crohn's disease (CD) remains to be a challenge due to limited insights for its pathogenesis. We aimed to determine the role of O-Linked β-N-acetylglucosamine (O-GlcNAc) in the development of CD and evaluate therapeutic effects of O-GlcNAc inhibitors on CD. Methods O-GlcNAc in intestinal epithelial tissues of CD, adherent-invasive Escherichia coli (AIEC) LF82-infected cells and mice was determined by immunoblot and immunohistochemistry. AIEC LF82 and dextran sulfate sodium were administrated into C57BL/6 mice for estabolishing inflammatory bowel disease model and for therapeutic study. Findings O-GlcNAc was increased in intestinal epithelial tissues of CD patients and AIEC LF82-infected mice. Infection of AIEC LF82 up-regulated the level of UDP-GlcNAc and increased O-GlcNAc in human colon epithelial HCT116 and HT-29 cells. We identified that IKKβ and NF-κB were O-Glycosylated in AIEC LF82-treated cells. Mutations of IKKβ (S733A) and p65 (T352A) abrogated the O-GlcNAc in IKKβ and NF-κB and inhibited AIEC LF82-induced activation of NF-κB. Application of 6-diazO-5-oxO-L-norleucine, an agent that blocks the production of UDP-GlcNAc and inhibits O-GlcNAc, inactivated NF-κB in AIEC LF82-infected cells, enhanced the formation of autophagy, promoted the removal of cell-associated AIEC LF82, alleviated intestinal epithelial inflammation, and improved the survival of the colitis mice. Interpretation Intestinal inflammation in CD is associated with increased O-GlcNAc modification, which is required for NF-κB activation and suppression of autophagy. Targeting O-GlcNAc could be an effective therapy for inflammatory bowel disease. Funding National Natural Science Foundation of China (Nos. 81573087 and 81772924) and International Cooperation Foundation of Jilin Province (20190701006GH).
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Perna A, Hay E, Contieri M, De Luca A, Guerra G, Lucariello A. Adherent-invasive Escherichia coli (AIEC): Cause or consequence of inflammation, dysbiosis, and rupture of cellular joints in patients with IBD? J Cell Physiol 2020; 235:5041-5049. [PMID: 31898324 DOI: 10.1002/jcp.29430] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022]
Abstract
There are many factors contributing to the development of gastrointestinal diseases, grouped into genetic, environmental, and lifestyle factors. In recent years attention has fallen on pathogens; in particular, Bacteroides fragilis, Fusobacterium nucleatum, Escherichia coli (E. coli) and Helicobacter pylori have been studied. Several points remain to be clarified, and above all, as regards the adherent-invasive E. coli strains of E. coli, one wonders if they are a cause or a consequence of the disease. In this review, we have tried to clarify some points by examining a series of recent publications regarding the involvement of the bacterium in the pathology, even if other studies are necessary.
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Affiliation(s)
- Angelica Perna
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Eleonora Hay
- Department of Mental and Physical Health and Preventive Medicine, Section of Human Anatomy, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Marcella Contieri
- Department of Mental and Physical Health and Preventive Medicine, Section of Human Anatomy, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Antonio De Luca
- Department of Mental and Physical Health and Preventive Medicine, Section of Human Anatomy, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Germano Guerra
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Angela Lucariello
- Department of Sport Sciences and Wellness, University of Naples "Parthenope", Naples, Italy
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30
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The role of major virulence factors and pathogenicity of adherent-invasive Escherichia coli in patients with Crohn's disease. GASTROENTEROLOGY REVIEW 2020; 15:279-288. [PMID: 33777266 PMCID: PMC7988836 DOI: 10.5114/pg.2020.93235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel disease (IBD) is a term that describes Crohn's disease (CD) and ulcerative colitis (UC), and these two conditions are characterised by chronic inflammation of the gastrointestinal tract. Dysbiosis of intestinal microbiota has been consistently linked to patients with IBD. In the last two decades, the progressive implication of adherent-invasive Escherichia coli (AIEC) pathogenesis in patients with CD has been increasing. Here we discuss recent findings that indicate the role and mechanisms of AIEC in IBD. We also highlight AIEC virulence factor genes and mechanisms that suggest an important role in the severity of inflammation in CD patients. Finally, we emphasise data on the prevalence of AIEC in CD patients.
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Integrating omics for a better understanding of Inflammatory Bowel Disease: a step towards personalized medicine. J Transl Med 2019; 17:419. [PMID: 31836022 PMCID: PMC6909475 DOI: 10.1186/s12967-019-02174-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/08/2019] [Indexed: 02/06/2023] Open
Abstract
Background Inflammatory Bowel Disease (IBD) is a multifactorial chronic disease. Understanding only one aspect of IBD pathogenesis does not reflect the complex nature of IBD nor will it improve its clinical management. Therefore, it is vital to dissect the interactions between the different players in IBD pathogenesis in order to understand the biology of the disease and enhance its clinical outcomes. Aims To provide an overview of the available omics data used to assess the potential mechanisms through which various players are contributing to IBD pathogenesis and propose a precision medicine model to fill the current knowledge gap in IBD. Results Several studies have reported microbial dysbiosis, immune and metabolic dysregulation in IBD patients, however, this data is not sufficient to create signatures that can differentiate between the disease subtypes or between disease relapse and remission. Conclusions We summarized the current knowledge in the application of omics in IBD patients, and we showed that the current knowledge gap in IBD hinders the improvements of clinical decision for treatment as well as the prediction of disease relapse. We propose one way to fill this gap by implementing integrative analysis of various omics datasets generated from one patient at a single time point.
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Lee JG, Han DS, Jo SV, Lee AR, Park CH, Eun CS, Lee Y. Characteristics and pathogenic role of adherent-invasive Escherichia coli in inflammatory bowel disease: Potential impact on clinical outcomes. PLoS One 2019; 14:e0216165. [PMID: 31034508 PMCID: PMC6488085 DOI: 10.1371/journal.pone.0216165] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/15/2019] [Indexed: 12/29/2022] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) has been reported as associated with the pathogenesis of inflammatory bowel disease (IBD). We aimed to investigate the characteristics of mucosa-associated E. coli and the clinical significance of AIEC in Korean IBD patients. E. coli strains were isolated from the mucosal tissues of 18 Crohn’s disease (CD) patients, 24 ulcerative colitis (UC) patients, and 9 healthy controls (HC). Adhesion, invasion, and survival assays were performed to evaluate phenotypic features of E. coli isolates and to identify AIEC. The presence of virulence genes and cytokine expression were examined using PCR. In addition, data on IBD-related hospitalization were collected. A total of 59 E. coli strains were isolated (25 from CD, 27 from UC, and 7 from HC). The average levels of adhesion, invasion, and survival were higher in E. coli strains from IBD patients than those from HC (adhesion: 1.65 vs. 0.71, p = 0.046; invasion: 1.68 vs. 0.52, p = 0.039; survival: 519.55 vs. 47.55, p = 0.363). Prevalence of AIEC in HC, CD and UC patients was 22.2%, 38.9% and 37.5%, respectively. E. coli isolates from IBD patients had various virulence genes and were associated with increased expression of TNF-α and IL-17. IBD-related hospitalization within 3 years was 18.8% in patients with AIEC and 11.5% in patients without AIEC. E. coli strains from IBD patients showed high levels of adhesion, invasion, and survival. AIEC strains were identified in both CD and UC patients at a similar rate. AIEC may be associated with sustaining inflammation in the pre-existing inflammatory mucosa.
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Affiliation(s)
- Jae Gon Lee
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea
| | - Dong Soo Han
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea
- * E-mail:
| | - Su Vin Jo
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea
| | - A. Reum Lee
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea
| | - Chan Hyuk Park
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea
| | - Chang Soo Eun
- Department of Internal Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea
| | - Yangsoon Lee
- Department of Laboratory Medicine, Hanyang University Hospital, Hanyang University College of Medicine, Seoul, Korea
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The Unique Lifestyle of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. J Mol Biol 2019; 431:2970-2981. [PMID: 31029703 DOI: 10.1016/j.jmb.2019.04.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/09/2019] [Accepted: 04/16/2019] [Indexed: 02/07/2023]
Abstract
Escherichia coli is one of the most genetically and phenotypically diverse species of bacteria. This remarkable diversity produces a plethora of clinical outcomes following infection and has informed much of what we currently know about host-pathogen interactions for a wide range of bacteria-host relationships. In studying the role of microbes in disease, adherent-invasive E. coli (AIEC) has emerged as having a strong association with Crohn's disease (CD). Thus, there has been an equally strong effort to uncover the root origins of AIEC, to appreciate how AIEC differs from other well-known pathogenic E. coli variants, and to understand its connection to disease. Emerging from a growing body of research on AIEC is the understanding that AIEC itself is remarkably diverse, both in phylogenetic origins, genetic makeup, and behavior in the host setting. Here, we describe the unique lifestyle of CD-associated AIEC and review recent research that is uncovering the inextricable link between AIEC and its host in the context of CD.
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Lepanto MS, Rosa L, Paesano R, Valenti P, Cutone A. Lactoferrin in Aseptic and Septic Inflammation. Molecules 2019; 24:molecules24071323. [PMID: 30987256 PMCID: PMC6480387 DOI: 10.3390/molecules24071323] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022] Open
Abstract
Lactoferrin (Lf), a cationic glycoprotein able to chelate two ferric irons per molecule, is synthesized by exocrine glands and neutrophils. Since the first anti-microbial function attributed to Lf, several activities have been discovered, including the relevant anti-inflammatory one, especially associated to the down-regulation of pro-inflammatory cytokines, as IL-6. As high levels of IL-6 are involved in iron homeostasis disorders, Lf is emerging as a potent regulator of iron and inflammatory homeostasis. Here, the role of Lf against aseptic and septic inflammation has been reviewed. In particular, in the context of aseptic inflammation, as anemia of inflammation, preterm delivery, Alzheimer’s disease and type 2 diabetes, Lf administration reduces local and/or systemic inflammation. Moreover, Lf oral administration, by decreasing serum IL-6, reverts iron homeostasis disorders. Regarding septic inflammation occurring in Chlamydia trachomatis infection, cystic fibrosis and inflammatory bowel disease, Lf, besides the anti-inflammatory activity, exerts a significant activity against bacterial adhesion, invasion and colonization. Lastly, a critical analysis of literature in vitro data reporting contradictory results on the Lf role in inflammatory processes, ranging from pro- to anti-inflammatory activity, highlighted that they depend on cell models, cell metabolic status, stimulatory or infecting agents as well as on Lf iron saturation degree, integrity and purity.
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Affiliation(s)
- Maria Stefania Lepanto
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy.
| | - Luigi Rosa
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy.
| | | | - Piera Valenti
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy.
| | - Antimo Cutone
- Department of Public Health and Infectious Diseases, University of Rome La Sapienza, 00185 Rome, Italy.
- Department of Biosciences and Territory, University of Molise, 86090 Pesche, Italy.
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Efficiency of Single Phage Suspensions and Phage Cocktail in the Inactivation of Escherichia coli and Salmonella Typhimurium: An In Vitro Preliminary Study. Microorganisms 2019; 7:microorganisms7040094. [PMID: 30935094 PMCID: PMC6518180 DOI: 10.3390/microorganisms7040094] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/22/2019] [Accepted: 03/27/2019] [Indexed: 01/09/2023] Open
Abstract
Enterobacteriaceae Escherichia coli and Salmonella enterica serovar Typhimurium strains are among the main pathogens responsible for moderate and serious infections at hospital and community environments, in part because they frequently present resistance to antibiotics. As the treatment of Enterobacteriaceae infections is empiric, using the same antibiotics to treat E. coli and Salmonella infections, the same concept can be applied with phages. The use of different phages combined in cocktails, frequently used to circumvent the development of phage-resistant mutants, also allows for the treatment of multiple pathogens, broadening the phages’ action spectrum. As such, the aim of this study was to evaluate the efficiency of a cocktail of two phages (ELY-1, produced on E. coli and phSE-5, produced on S. Typhimurium) to control E. coli and S. Typhimurium. Phages ELY-1 and phSE-5 were effective against E. coli (maximum reductions of 4.5 and 3.8 log CFU/mL, respectively), S. Typhimurium (maximum reductions of 2.2 and 2.6 log CFU/mL, respectively), and the mixture of both bacteria (maximum reductions of 2.2 and 2.0 log CFU/mL, respectively). The cocktail ELY-1/phSE-5 was more effective against S. Typhimurium and the mixture of both bacteria (maximum reduction of 3.2 log CFU/mL for both) than the single phage suspensions and as effective against E. coli as its specific phage ELY-1 (maximum reductions of 4.5 log CFU/mL). The use of both the phage cocktails, as well as the single-phage suspensions, however, did not prevent the occurrence of phage-resistant mutants. Overall, the results indicate that the application of the phages in the form of a cocktail show their potential to be used presumptively, that is, prior to the identification of the pathogens, paving its use to control E. coli or S. Typhimurium.
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Camprubí-Font C, Ewers C, Lopez-Siles M, Martinez-Medina M. Genetic and Phenotypic Features to Screen for Putative Adherent-Invasive Escherichia coli. Front Microbiol 2019; 10:108. [PMID: 30846972 PMCID: PMC6393329 DOI: 10.3389/fmicb.2019.00108] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/18/2019] [Indexed: 01/19/2023] Open
Abstract
To date no molecular tools are available to identify the adherent-invasive Escherichia coli (AIEC) pathotype, which has been associated with Crohn’s disease and colonizes the intestine of different hosts. Current techniques based on phenotypic screening of isolates are extremely time-consuming. The aim of this work was to search for signature traits to assist in rapid AIEC identification. The occurrence of at least 54 virulence genes (VGs), the resistance to 30 antibiotics and the distribution of FimH and ChiA amino acid substitutions was studied in a collection of 48 AIEC and 56 non-AIEC isolated from the intestine of humans and animals. χ2 test was used to find frequency differences according to origin of isolation, AIEC phenotype and phylogroup. Mann–Whitney test was applied to test association with adhesion and invasion indices. Binary logistic regression was performed to search for variables of predictive value. Animal strains (N = 45) were enriched in 12 VGs while 7 VGs were more predominant in human strains (N = 59). The prevalence of 15 VGs was higher in AIEC (N = 49) than in non-AIEC (N = 56) strains, but only pic gene was still differentially distributed when analyzing human and animal strains separately. Among human strains, three additional VGs presented higher frequency in AIEC strains (papGII/III, iss and vat; N = 22) than in non-AIEC strains (N = 37). No differences between AIEC/non-AIEC were found in FimH variants. In contrast, the ChiA sequence of LF82 was shared with the 35.5% of AIEC studied (N = 31) and only with the 7.4% of non-AIEC strains (N = 27; p = 0.027). Binary logistic regression analysis, using as input variables all the VGs and antibiotic resistances tested, revealed that typifying E. coli isolates using pic gene and ampicillin resistance was useful to correctly classify strains according to the phenotype with a 75.5% of accuracy. Although there is not a molecular signature fully specific and sensitive to identify the AIEC pathotype, we propose two features easy to be tested that could assist in AIEC screening. Future work using additional strain collections would be required to assess the applicability of this method.
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Affiliation(s)
- Carla Camprubí-Font
- Laboratory of Molecular Microbiology, Department of Biology, Universitat de Girona, Girona, Spain
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, Giessen, Germany
| | - Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Department of Biology, Universitat de Girona, Girona, Spain
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Lopes A, Pereira C, Almeida A. Sequential Combined Effect of Phages and Antibiotics on the Inactivation of Escherichia coli. Microorganisms 2018; 6:E125. [PMID: 30563133 PMCID: PMC6313441 DOI: 10.3390/microorganisms6040125] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/28/2018] [Accepted: 12/03/2018] [Indexed: 12/17/2022] Open
Abstract
The emergence of antibiotic resistance in bacteria is a global concern. The use of bacteriophages (or phages) alone or combined with antibiotics is consolidating itself as an alternative approach to inactivate antibiotic-resistant bacteria. However, phage-resistant mutants have been considered as a major threat when phage treatment is employed. Escherichia coli is one of the main responsible pathogens for moderate and serious infections in hospital and community environments, being involved in the rapid evolution of fluoroquinolones and third-generation cephalosporin resistance. The aim of this study was to evaluate the effect of combined treatments of phages and antibiotics in the inactivation of E. coli. For this, ciprofloxacin at lethal and sublethal concentrations was added at different times (0, 6, 12 and 18 h) and was tested in combination with the phage ELY-1 to inactivate E. coli. The efficacy of the combined treatment varied with the antibiotic concentration and with the time of antibiotic addition. The combined treatment prevented bacterial regrowth when the antibiotic was used at minimum inhibitory concentration (MIC) and added after 6 h of phage addition, causing less bacterial resistance than phage and antibiotic applied alone (4.0 × 10-7 for the combined treatment, 3.9 × 10-6 and 3.4 × 10-5 for the antibiotics and the phages alone, respectively). Combined treatment with phage and antibiotic can be effective in reducing the bacterial density and it can also prevent the emergence of resistant variants. However, the antibiotic concentration and the time of antibiotic application are essential factors that need to be considered in the combined treatment.
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Affiliation(s)
- Ana Lopes
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Carla Pereira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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Eissa N, Kittana H, Gomes-Neto JC, Hussein H. Mucosal immunity and gut microbiota in dogs with chronic enteropathy. Res Vet Sci 2018; 122:156-164. [PMID: 30504001 DOI: 10.1016/j.rvsc.2018.11.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/19/2018] [Accepted: 11/23/2018] [Indexed: 12/18/2022]
Abstract
Chronic enteropathy (CE) in dogs is a chronic and relapsing immunopathology, of unknown etiology, that usually manifests with a plethora of clinical signs reflecting the underlying heterogeneity in its pathogenesis. Alterations of the mucosal immune responses and the gut microbiota composition are thought to play an essential role in CE. Similar to humans, it is hypothesized that the breakdown in mucosal tolerance leads to aberrant and pathological immune responses toward the gut microbiota, that in turn, may contribute to the severity of disease, at least for certain CE subsets. Therefore, in this review, we discuss some of the most relevant and recent insights microbiological and immunological aspects characterizing CE in dogs.
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Affiliation(s)
- Nour Eissa
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.
| | - Hatem Kittana
- Department of Food Science and Technology, University of Nebraska-, Lincoln, NE, USA
| | - João Carlos Gomes-Neto
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
| | - Hayam Hussein
- Department of Parasitology and Animal Diseases, Veterinary Research Division, National Research Centre, Giza, Egypt
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Rahmouni O, Vignal C, Titécat M, Foligné B, Pariente B, Dubuquoy L, Desreumaux P, Neut C. High carriage of adherent invasive E. coli in wildlife and healthy individuals. Gut Pathog 2018; 10:23. [PMID: 29946365 PMCID: PMC6001069 DOI: 10.1186/s13099-018-0248-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/23/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Adherent invasive Escherichia coli (AIEC) are suspected to be involved in the pathogenesis of inflammatory bowel diseases. Since AIEC was first described in 1999, despite important progress on its genomic and immune characterizations, some crucial questions remain unanswered, such as whether there exists a natural reservoir, or whether there is asymptomatic carriage. The ECOR collection, including E. coli strains isolated mainly from the gut of healthy humans and animals, constitutes an ideal tool to investigate AIEC prevalence in healthy condition. A total of 61 E. coli strains were examined for characteristics of AIEC. METHODS The adhesion, invasion and intramacrophage replication capabilities (AIEC phenotype) of 61 intestinal E. coli strains were determined. The absence of virulence-associated diarrheagenic E. coli pathotypes (EPEC, ETEC, EIEC, EHEC, DAEC, EAEC), and uropathogenic E. coli was checked. RESULTS Out of 61 intestinal strains, 13 (21%) exhibit the AIEC phenotype, 7 are from human origin and 6 are from animal origin. Prevalence of AIEC strains is about 24 and 19% in healthy humans and animals respectively. These strains are highly genetically diverse as they are distributed among the main described phylogroups. Among E. coli strains from the ECOR collection, we also detected strains able to detach I-407 cells. CONCLUSIONS Our study described for the first time AIEC strains isolated from the feces of healthy humans and animals.
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Affiliation(s)
- Oumaïra Rahmouni
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
| | - Cécile Vignal
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
| | - Marie Titécat
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
- Centre de Biologie Pathologie Génétique, CHU Lille, Lille, France
| | - Benoît Foligné
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
| | - Benjamin Pariente
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
- Service des Maladies de l’Appareil Digestif et de la Nutrition, Hôpital Claude Huriez, CHU Lille, 59037 Lille, France
| | - Laurent Dubuquoy
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
| | - Pierre Desreumaux
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
- Service des Maladies de l’Appareil Digestif et de la Nutrition, Hôpital Claude Huriez, CHU Lille, 59037 Lille, France
| | - Christel Neut
- Lille Inflammation Research International Center, UMR 995 Inserm, Lille University, CHRU Lille, Lille, France
- Laboratoire de Bactériologie, 3, Rue de Pr. Laguesse, B.P. 83, 59006 Lille Cedex, France
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Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC SYSTEMS BIOLOGY 2018; 12:66. [PMID: 29890970 PMCID: PMC5996543 DOI: 10.1186/s12918-018-0587-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/21/2018] [Indexed: 01/04/2023]
Abstract
Background Escherichia coli is considered a leading bacterial trigger of inflammatory bowel disease (IBD). E. coli isolates from IBD patients primarily belong to phylogroup B2. Previous studies have focused on broad comparative genomic analysis of E. coli B2 isolates, and identified virulence factors that allow B2 strains to reside within human intestinal mucosa. Metabolic capabilities of E. coli strains have been shown to be related to their colonization site, but remain unexplored in IBD-associated strains. Results In this study, we utilized pan-genome analysis and genome-scale models (GEMs) of metabolism to study metabolic capabilities of IBD-associated E. coli B2 strains. The study yielded three results: i) Pan-genome analysis of 110 E. coli strains (including 53 isolates from IBD studies) revealed discriminating metabolic genes between B2 strains and other strains; ii) Both comparative genomic analysis and GEMs suggested that B2 strains have an advantage in degrading and utilizing sugars derived from mucus glycan, and iii) GEMs revealed distinct metabolic features in B2 strains that potentially allow them to utilize energy more efficiently. For example, B2 strains lack the enzymes to degrade amadori products, but instead rely on neighboring bacteria to convert these substrates into a more readily usable and potentially less sought after product. Conclusions Taken together, these results suggest that the metabolic capabilities of B2 strains vary significantly from those of other strains, enabling B2 strains to colonize intestinal mucosa.The results from this study motivate a broad experimental assessment of the nutritional effects on E. coli B2 pathophysiology in IBD patients. Electronic supplementary material The online version of this article (10.1186/s12918-018-0587-5) contains supplementary material, which is available to authorized users.
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Azimi T, Nasiri MJ, Chirani AS, Pouriran R, Dabiri H. The role of bacteria in the inflammatory bowel disease development: a narrative review. APMIS 2018; 126:275-283. [DOI: 10.1111/apm.12814] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/16/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Taher Azimi
- Department of Pathobiology; School of Public Health; Tehran University of Medical Sciences; Tehran Iran
| | - Mohammad Javad Nasiri
- Department of Medical Microbiology; School of Medicine; Shahid Beheshti University of Medical Sciences; Tehran Iran
| | - Alireza Salimi Chirani
- Department of Medical Microbiology; School of Medicine; Shahid Beheshti University of Medical Sciences; Tehran Iran
| | - Ramin Pouriran
- School of Medicine; Shahid Beheshti University of Medical Sciences; Tehran Iran
| | - Hossein Dabiri
- Department of Medical Microbiology; School of Medicine; Shahid Beheshti University of Medical Sciences; Tehran Iran
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Palmela C, Chevarin C, Xu Z, Torres J, Sevrin G, Hirten R, Barnich N, Ng SC, Colombel JF. Adherent-invasive Escherichia coli in inflammatory bowel disease. Gut 2018; 67:574-587. [PMID: 29141957 DOI: 10.1136/gutjnl-2017-314903] [Citation(s) in RCA: 309] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/20/2017] [Accepted: 10/28/2017] [Indexed: 02/06/2023]
Abstract
Intestinal microbiome dysbiosis has been consistently described in patients with IBD. In the last decades, Escherichia coli, and the adherent-invasive E coli (AIEC) pathotype in particular, has been implicated in the pathogenesis of IBD. Since the discovery of AIEC, two decades ago, progress has been made in unravelling these bacteria characteristics and its interaction with the gut immune system. The mechanisms of adhesion of AIEC to intestinal epithelial cells (via FimH and cell adhesion molecule 6) and its ability to escape autophagy when inside macrophages are reviewed here. We also explore the existing data on the prevalence of AIEC in patients with Crohn's disease and UC, and the association between the presence of AIEC and disease location, activity and postoperative recurrence. Finally, we highlight potential therapeutic strategies targeting AIEC colonisation of gut mucosa, including the use of phage therapy, bacteriocins and antiadhesive molecules. These strategies may open new avenues for the prevention and treatment of IBD in the future.
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Affiliation(s)
- Carolina Palmela
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Caroline Chevarin
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Zhilu Xu
- Department of Medicine and Therapeutics, Institute of Digestive Diseases, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Joana Torres
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA.,Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Gwladys Sevrin
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Robert Hirten
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, USC-INRA 2018, M2iSH, CRNH Auvergne, F-63000 Clermont-Ferrand, France
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Diseases, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
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Investigation of adherent-invasive E. coli in patients with Crohn's disease. Med J Islam Repub Iran 2018; 32:11. [PMID: 30159262 PMCID: PMC6108281 DOI: 10.14196/mjiri.32.11] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Indexed: 02/07/2023] Open
Abstract
Background: Crohn's disease and Ulcerative colitis are known as inflammatory bowel disease with high morbidity which are as a result of increasing immune responses to intestinal microbiota in genetically susceptible individuals. The association of adherent invasive Escherichia coli with Crohn's disease in human has been discussed for decades. The principal aim of this study was to assess the relationship between adherent invasive Escherichia coli in Iranian patients with Crohn's disease.
Methods: The presence of adherent invasive Escherichia coli DNA and viable adherent invasive Escherichia coli cells were identified through PCR and conventional culture methods, respectively. All the specimens were subsequently cultured in Hi Chrome Agar medium.
Results: Using molecular assay, the invasive plasmid antigen H and invasion-association locus genes were detected from tissue samples confirming the presence of adherent-invasive Escherichia coli. The invasive plasmid antigen H was detected in 46.7% of CD and 13.3% of healthy peoples. The invasion-association locus gene was found in 36.7% of patients with Crohn's disease and 10% in individuals without IBD.
Conclusion: This study demonstrated an increased frequency of adherent invasive E. coli with invasive plasmid antigen H and invasion-association locus genes from patients with CD in comparison to control individuals. Moreover, it was shown that adherent invasive E. coli with the invasive plasmid antigen H and invasion-association locus genes can act as a predisposing factor in the development of IBD.
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Comparative genomics reveals new single-nucleotide polymorphisms that can assist in identification of adherent-invasive Escherichia coli. Sci Rep 2018; 8:2695. [PMID: 29426864 PMCID: PMC5807354 DOI: 10.1038/s41598-018-20843-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/24/2018] [Indexed: 01/19/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) have been involved in Crohn’s disease (CD). Currently, AIEC are identified by time-consuming techniques based on in vitro infection of cell lines to determine their ability to adhere to and invade intestinal epithelial cells as well as to survive and replicate within macrophages. Our aim was to find signature sequences that can be used to identify the AIEC pathotype. Comparative genomics was performed between three E. coli strain pairs, each pair comprised one AIEC and one non-AIEC with identical pulsotype, sequence type and virulence gene carriage. Genetic differences were further analysed in 22 AIEC and 28 non-AIEC isolated from CD patients and controls. The strain pairs showed similar genome structures, and no gene was specific to AIEC. Three single nucleotide polymorphisms displayed different nucleotide distributions between AIEC and non-AIEC, and four correlated with increased adhesion and/or invasion indices. Here, we present a classification algorithm based on the identification of three allelic variants that can predict the AIEC phenotype with 84% accuracy. Our study corroborates the absence of an AIEC-specific genetic marker distributed across all AIEC strains. Nonetheless, point mutations putatively involved in the AIEC phenotype can be used for the molecular identification of the AIEC pathotype.
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Antibiotics and Phage Sensitivity as Interventions for Controlling Escherichia coli Isolated from Clinical Specimens. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2017. [DOI: 10.22207/jpam.11.4.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Sarshar M, Scribano D, Marazzato M, Ambrosi C, Aprea MR, Aleandri M, Pronio A, Longhi C, Nicoletti M, Zagaglia C, Palamara AT, Conte MP. Genetic diversity, phylogroup distribution and virulence gene profile of pks positive Escherichia coli colonizing human intestinal polyps. Microb Pathog 2017; 112:274-278. [PMID: 28987619 DOI: 10.1016/j.micpath.2017.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/05/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023]
Abstract
Some Escherichia coli strains of phylogroup B2 harbor a (pks) pathogenicity island that encodes a polyketide-peptide genotoxin called colibactin. It causes DNA double-strand breaks and megalocytosis in eukaryotic cells and it may contribute to cancer development. Study of bacterial community that colonizes the adenomatous polyp lesion, defined as precancerous lesions, could be helpful to assess if such pathogenic bacteria possess a role in the polyp progression to cancer. In this cross-sectional study, a total of 1500 E. coli isolates were obtained from biopsies of patients presenting adenomatous colon polyps, the normal tissues adjacent to the polyp lesion and patients presenting normal mucosa. pks island frequency, phylogenetic grouping, fingerprint genotyping, and virulence gene features of pks positive (pks+) E. coli isolates were performed. We found pks+E. coli strongly colonize two patients presenting polypoid lesions and none were identified in patients presenting normal mucosa. Predominant phylogroups among pks+E. coli isolates were B2, followed by D. Clustering based on fragment profiles of composite analysis, typed the pks+ isolates into 5 major clusters (I-V) and 17 sub-clusters, demonstrating a high level of genetic diversity among them. The most prevalent virulence genes were fimH and fyuA (100%), followed by vat (92%), hra and papA (69%), ibeA (28%), and hlyA (25%). Our results revealed that pks+E. coli can colonize the precancerous lesions, with a high distribution in both the polyp lesions and in normal tissues adjacent to the lesion. The high differences in fingerprinting patterns obtained indicate that pks+E. coli strains were genetically diverse, possibly allowing them to more easily adapt to environmental variations.
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Affiliation(s)
- Meysam Sarshar
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory Affiliated to Institute Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy; Department of Medical, Oral and Biotechnological Sciences, University "G. D'Annunzio" of Chieti, Chieti, Italy.
| | - Massimiliano Marazzato
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Cecilia Ambrosi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Maria Rita Aprea
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Marta Aleandri
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Annamaria Pronio
- Department of General Surgery, "P. Stefanini", Sapienza University of Rome, Rome, Italy
| | - Catia Longhi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Mauro Nicoletti
- Department of Medical, Oral and Biotechnological Sciences, University "G. D'Annunzio" of Chieti, Chieti, Italy
| | - Carlo Zagaglia
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Anna Teresa Palamara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory Affiliated to Institute Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy; San Raffaele Pisana IRCCS, Telematic University, Rome, Italy
| | - Maria Pia Conte
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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Abstract
The human gut is home to trillions of bacteria and provides the scaffold for one of the most complex microbial ecosystems in nature. Inflammatory bowel diseases, such as Crohn's disease, involve a compositional shift in the microbial constituents of this ecosystem with a marked expansion of Enterobacteriaceae, particularly Escherichia coli. Adherent-invasive E. coli (AIEC) strains are frequently isolated from the biopsies of Crohn's patients, where their ability to elicit inflammation suggests a possible role in Crohn's pathology. Here, we consider the origins of the AIEC pathovar and discuss how risk factors associated with Crohn's disease might influence AIEC colonization dynamics within the host to alter the overall disease potential of the microbial community.
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Affiliation(s)
- Wael Elhenawy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada,Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Alexander Oberc
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada,Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada
| | - Brian K. Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada,Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, ON, Canada,CONTACT Brian K. Coombes , Department of Biochemistry and Biomedical Sciences, McMaster University, MDCL 2319, Hamilton, ON Canada L8S 4K1
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Sivignon A, Bouckaert J, Bernard J, Gouin SG, Barnich N. The potential of FimH as a novel therapeutic target for the treatment of Crohn’s disease. Expert Opin Ther Targets 2017; 21:837-847. [DOI: 10.1080/14728222.2017.1363184] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Adeline Sivignon
- M2iSH, UMR 1071 Inserm, INRA USC-2018, Institut Universitaire Technologique, Université Clermont Auvergne, Clermont-Ferrand 63001, France
| | - Julie Bouckaert
- Univ. Lille, CNRS, UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Julien Bernard
- Université de Lyon, Lyon, France ; INSA-Lyon, Ingénierie des Matériaux Polymères (IMP), Villeurbanne, France ; CNRS, UMR 5223, Ingénierie des Matériaux Polymères, Villeurbanne, France
- INSA-Lyon, IMP, Villeurbanne, France
- UMR 5223, Ingénierie des Matériaux Polymères, CNRS, Villeurbanne, France
| | - Sebastien G. Gouin
- CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, LUNAM Université, Nantes Cedex 3, France
| | - Nicolas Barnich
- M2iSH, UMR 1071 Inserm, INRA USC-2018, Institut Universitaire Technologique, Université Clermont Auvergne, Clermont-Ferrand 63001, France
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O'Brien CL, Bringer MA, Holt KE, Gordon DM, Dubois AL, Barnich N, Darfeuille-Michaud A, Pavli P. Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli. Gut 2017; 66:1382-1389. [PMID: 27196580 DOI: 10.1136/gutjnl-2015-311059] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 03/22/2016] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Adherent-invasive Escherichia coli (AIEC) are a leading candidate bacterial trigger for Crohn's disease (CD). The AIEC pathovar is defined by in vitro cell-line assays examining specific bacteria/cell interactions. No molecular marker exists for their identification. Our aim was to identify a molecular property common to the AIEC phenotype. DESIGN 41 B2 phylogroup E. coli strains were isolated from 36 Australian subjects: 19 patients with IBD and 17 without. Adherence/invasion assays were conducted using the I-407 epithelial cell line and survival/replication assays using the THP-1 macrophage cell line. Cytokine secretion tumour necrosis factor ((TNF)-α, interleukin (IL) 6, IL-8 and IL-10) was measured using ELISA. The genomes were assembled and annotated, and cluster analysis performed using CD-HIT. The resulting matrices were analysed to identify genes unique/more frequent in AIEC strains compared with non-AIEC strains. Base composition differences and clustered regularly interspaced palindromic repeat (CRISPR) analyses were conducted. RESULTS Of all B2 phylogroup strains assessed, 79% could survive and replicate in macrophages. Among them, 11/41 strains (5 CD, 2 UCs, 5 non-IBD) also adhere to and invade epithelial cells, a phenotype assigning them to the AIEC pathovar. The AIEC strains were phylogenetically heterogeneous. We did not identify a gene (or nucleic acid base composition differences) common to all, or the majority of, AIEC. Cytokine secretion and CRISPRs were not associated with the AIEC phenotype. CONCLUSIONS Comparative genomic analysis of AIEC and non-AIEC strains did not identify a molecular property exclusive to the AIEC phenotype. We recommend a broader approach to the identification of the bacteria-host interactions that are important in the pathogenesis of Crohn's disease.
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Affiliation(s)
- Claire L O'Brien
- Medical School, Australian National University, Canberra, Australian Capital Territory, Australia.,Gastroenterology and Hepatology Unit, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Marie-Agnès Bringer
- INRA UMR1324, CNRS UMR6265, Université Bourgogne-Franche-Comté, Centre des Sciences du Goût et de l'Alimentation, Dijon, France.,UMR1071 Inserm/University of Auvergne, INRA USC2018, M2iSH, Clermont-Ferrand, France
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - David M Gordon
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Anaëlle L Dubois
- UMR1071 Inserm/University of Auvergne, INRA USC2018, M2iSH, Clermont-Ferrand, France
| | - Nicolas Barnich
- UMR1071 Inserm/University of Auvergne, INRA USC2018, M2iSH, Clermont-Ferrand, France
| | | | - Paul Pavli
- Medical School, Australian National University, Canberra, Australian Capital Territory, Australia.,Gastroenterology and Hepatology Unit, Canberra Hospital, Canberra, Australian Capital Territory, Australia
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50
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Rakitina DV, Manolov AI, Kanygina AV, Garushyants SK, Baikova JP, Alexeev DG, Ladygina VG, Kostryukova ES, Larin AK, Semashko TA, Karpova IY, Babenko VV, Ismagilova RK, Malanin SY, Gelfand MS, Ilina EN, Gorodnichev RB, Lisitsyna ES, Aleshkin GI, Scherbakov PL, Khalif IL, Shapina MV, Maev IV, Andreev DN, Govorun VM. Genome analysis of E. coli isolated from Crohn's disease patients. BMC Genomics 2017; 18:544. [PMID: 28724357 PMCID: PMC5517970 DOI: 10.1186/s12864-017-3917-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/02/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn's disease (CD). The phylogeny of E. coli isolated from Crohn's disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. RESULTS We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons. CONCLUSIONS Our findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols.
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Affiliation(s)
- Daria V. Rakitina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Alexander I. Manolov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | | | - Sofya K. Garushyants
- Skolkovo Institute of Science and Technology, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Julia P. Baikova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry G. Alexeev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute for Physics and Technology, Moscow, Russia
| | - Valentina G. Ladygina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Elena S. Kostryukova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrei K. Larin
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Tatiana A. Semashko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Irina Y. Karpova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vladislav V. Babenko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ruzilya K. Ismagilova
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Fundamental Medicine and Biology of Kazan Federal University, Kazan, Russia
| | - Sergei Y. Malanin
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Fundamental Medicine and Biology of Kazan Federal University, Kazan, Russia
| | - Mikhail S. Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Computer Science, National Research University Higher School of Economics, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Elena N. Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Roman B. Gorodnichev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Eugenia S. Lisitsyna
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Gennady I. Aleshkin
- The Gamaleya Research Institute for Epidemiology and Microbiology of the Russian Academy of Medical Science, Moscow, Russia
| | - Petr L. Scherbakov
- Central Scientific Institute of Gastroenterology, Moscow Clinical Research Centre, Moscow, Russia
| | - Igor L. Khalif
- State Scientific Center of Coloproctology, Ministry of Health of Russian Federation, Moscow, Russia
| | - Marina V. Shapina
- State Scientific Center of Coloproctology, Ministry of Health of Russian Federation, Moscow, Russia
| | - Igor V. Maev
- Moscow State University of Medicine and Dentistry named after A.I. Evdokimov, Ministry of Health of Russian Federation, Moscow, Russia
| | - Dmitry N. Andreev
- Moscow State University of Medicine and Dentistry named after A.I. Evdokimov, Ministry of Health of Russian Federation, Moscow, Russia
| | - Vadim M. Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute for Physics and Technology, Moscow, Russia
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