51
|
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.
Collapse
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
| |
Collapse
|
52
|
Khan AA, Khan Z, Malik A, Kalam MA, Cash P, Ashraf MT, Alshamsan A. Colorectal cancer-inflammatory bowel disease nexus and felony of Escherichia coli. Life Sci 2017; 180:60-67. [PMID: 28506682 DOI: 10.1016/j.lfs.2017.05.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 04/24/2017] [Accepted: 05/12/2017] [Indexed: 12/19/2022]
Abstract
Colorectal cancer (CRC) has a multifactorial etiology. Although the exact cause of CRC is still elusive, recent studies have indicated microbial involvement in its etiology. Escherichia coli has emerged as an important factor in CRC development since the bacterium can cause changes in the gut that lead to cancerous transformation. A number of studies indicate that chronic inflammation induced by microorganisms, including E. coli, during inflammatory bowel disease (IBD) predisposes an individual to CRC. The evidence that support the role of E. coli in the etiology of CRC, through IBD, is not limited only to chronic inflammation. The growth of E. coli as an intracellular pathogen during IBD and CRC enable the bacteria to modulate the host cell cycle, induce DNA damage and accumulate mutations. These are some of the contributing factors behind the etiology of CRC. The present article considers the current status of the involvement of E. coli, through IBD, in the etiology of CRC. We discuss how intracellular E. coli infection can cause changes in the gut that can eventually lead to cellular transformation. In addition, the recent management strategies that target E. coli for prevention of CRC are also discussed.
Collapse
Affiliation(s)
- Abdul Arif Khan
- Nanomedicine Research Unit, Department of Pharmaceutics, College of Pharmacy, PO Box 2457, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Zakir Khan
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Baverly Blvd., Los Angeles, CA 90048, USA
| | - Abdul Malik
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohd Abul Kalam
- Nanomedicine Research Unit, Department of Pharmaceutics, College of Pharmacy, PO Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
| | - Phillip Cash
- The Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | | | - Aws Alshamsan
- Nanomedicine Research Unit, Department of Pharmaceutics, College of Pharmacy, PO Box 2457, King Saud University, Riyadh 11451, Saudi Arabia; King Abdullah Institute for Nanotechnology, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| |
Collapse
|
53
|
Viladomiu M, Kivolowitz C, Abdulhamid A, Dogan B, Victorio D, Castellanos JG, Woo V, Teng F, Tran NL, Sczesnak A, Chai C, Kim M, Diehl GE, Ajami NJ, Petrosino JF, Zhou XK, Schwartzman S, Mandl LA, Abramowitz M, Jacob V, Bosworth B, Steinlauf A, Scherl EJ, Wu HJJ, Simpson KW, Longman RS. IgA-coated E. coli enriched in Crohn's disease spondyloarthritis promote T H17-dependent inflammation. Sci Transl Med 2017; 9:eaaf9655. [PMID: 28179509 PMCID: PMC6159892 DOI: 10.1126/scitranslmed.aaf9655] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 08/12/2016] [Accepted: 12/27/2016] [Indexed: 12/21/2022]
Abstract
Peripheral spondyloarthritis (SpA) is a common extraintestinal manifestation in patients with active inflammatory bowel disease (IBD) characterized by inflammatory enthesitis, dactylitis, or synovitis of nonaxial joints. However, a mechanistic understanding of the link between intestinal inflammation and SpA has yet to emerge. We evaluated and functionally characterized the fecal microbiome of IBD patients with or without peripheral SpA. Coupling the sorting of immunoglobulin A (IgA)-coated microbiota with 16S ribosomal RNA-based analysis (IgA-seq) revealed a selective enrichment in IgA-coated Escherichia coli in patients with Crohn's disease-associated SpA (CD-SpA) compared to CD alone. E. coli isolates from CD-SpA-derived IgA-coated bacteria were similar in genotype and phenotype to an adherent-invasive E. coli (AIEC) pathotype. In comparison to non-AIEC E. coli, colonization of germ-free mice with CD-SpA E. coli isolates induced T helper 17 cell (TH17) mucosal immunity, which required the virulence-associated metabolic enzyme propanediol dehydratase (pduC). Modeling the increase in mucosal and systemic TH17 immunity we observed in CD-SpA patients, colonization of interleukin-10-deficient or K/BxN mice with CD-SpA-derived E. coli lead to more severe colitis or inflammatory arthritis, respectively. Collectively, these data reveal the power of IgA-seq to identify immunoreactive resident pathosymbionts that link mucosal and systemic TH17-dependent inflammation and offer microbial and immunophenotype stratification of CD-SpA that may guide medical and biologic therapy.
Collapse
Affiliation(s)
- Monica Viladomiu
- Jill Roberts Institute for Research in Inflammatory Bowel Disease (IBD), Weill Cornell Medicine, New York, NY 10021, USA
| | - Charles Kivolowitz
- Jill Roberts Institute for Research in Inflammatory Bowel Disease (IBD), Weill Cornell Medicine, New York, NY 10021, USA
| | - Ahmed Abdulhamid
- Jill Roberts Institute for Research in Inflammatory Bowel Disease (IBD), Weill Cornell Medicine, New York, NY 10021, USA
| | - Belgin Dogan
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Daniel Victorio
- Jill Roberts Institute for Research in Inflammatory Bowel Disease (IBD), Weill Cornell Medicine, New York, NY 10021, USA
| | - Jim G Castellanos
- Jill Roberts Institute for Research in Inflammatory Bowel Disease (IBD), Weill Cornell Medicine, New York, NY 10021, USA
| | - Viola Woo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease (IBD), Weill Cornell Medicine, New York, NY 10021, USA
| | - Fei Teng
- Department of Immunobiology, University of Arizona, Tucson, AZ 85719, USA
| | - Nhan L Tran
- Department of Immunobiology, University of Arizona, Tucson, AZ 85719, USA
| | - Andrew Sczesnak
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94709, USA
| | - Christina Chai
- Jill Roberts Institute for Research in Inflammatory Bowel Disease (IBD), Weill Cornell Medicine, New York, NY 10021, USA
| | - Myunghoo Kim
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gretchen E Diehl
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xi K Zhou
- Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York, NY 10065, USA
| | | | - Lisa A Mandl
- Hospital for Special Surgery, New York, NY 10021, USA
| | - Meira Abramowitz
- Jill Roberts Center for IBD, Weill Cornell Medicine, New York, NY 10021, USA
| | - Vinita Jacob
- Jill Roberts Center for IBD, Weill Cornell Medicine, New York, NY 10021, USA
| | - Brian Bosworth
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Adam Steinlauf
- Jill Roberts Center for IBD, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ellen J Scherl
- Jill Roberts Center for IBD, Weill Cornell Medicine, New York, NY 10021, USA
| | - Hsin-Jung Joyce Wu
- Department of Immunobiology, University of Arizona, Tucson, AZ 85719, USA
| | - Kenneth W Simpson
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Randy S Longman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease (IBD), Weill Cornell Medicine, New York, NY 10021, USA.
- Jill Roberts Center for IBD, Weill Cornell Medicine, New York, NY 10021, USA
| |
Collapse
|
54
|
Vasovic M, Gajovic N, Brajkovic D, Jovanovic M, Zdravkovaic N, Kanjevac T. The relationship between the immune system and oral manifestations of inflammatory bowel disease: a review. Cent Eur J Immunol 2016; 41:302-310. [PMID: 27833449 PMCID: PMC5099388 DOI: 10.5114/ceji.2016.63131] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 07/28/2015] [Indexed: 12/15/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are chronic, relapsing inflammatory diseases characterized by exacerbations and remissions of the gastrointestinal tract, clinically manifested as Crohn's disease and ulcerative colitis. The etiology of IBDs is considered to be multi factorial, comprising environmental, immune, microbial and genetic factors. Clinical signs may include abdominal pain, frequent bloody diarrheas, mucorrhea, vomiting, fever, fatigue or weight loss. Changes in the oral cavity often precede intestinal symptoms. Inflammatory bowel disease leads to a significant deterioration of oral health, which indicates that cooperation between the dentist and the gastroenterologist is necessary when considering patients' welfare. Patients with IBD have an altered immune response, but microorganisms of the oral cavity may also be responsible for its modification. This review paper discusses the correlation between the immune system and inflammatory bowel disease manifestations in the oral cavity.
Collapse
Affiliation(s)
- Miroslav Vasovic
- Department of Dentistry, Faculty of Medical Sciences, University of Kragujevac, Serbia
| | - Nevena Gajovic
- Center for Molecular Medicine and Stem Cells Research, Faculty of Medical Sciences, University of Kragujevac, Serbia
| | - Denis Brajkovic
- Department of Dentistry, Faculty of Medical Sciences, University of Kragujevac, Serbia
| | - Marina Jovanovic
- Department of Internal Medicine, Faculty of Medical Sciences, University of Kragujevac, Serbia
| | - Natasa Zdravkovaic
- Department of Internal Medicine, Faculty of Medical Sciences, University of Kragujevac, Serbia
| | - Tatjana Kanjevac
- Department of Dentistry, Faculty of Medical Sciences, University of Kragujevac, Serbia
| |
Collapse
|
55
|
Small CL, Xing L, McPhee JB, Law HT, Coombes BK. Acute Infectious Gastroenteritis Potentiates a Crohn's Disease Pathobiont to Fuel Ongoing Inflammation in the Post-Infectious Period. PLoS Pathog 2016; 12:e1005907. [PMID: 27711220 PMCID: PMC5053483 DOI: 10.1371/journal.ppat.1005907] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/30/2016] [Indexed: 12/18/2022] Open
Abstract
Crohn’s disease (CD) is a chronic inflammatory condition of diverse etiology. Exposure to foodborne pathogens causing acute gastroenteritis produces a long-term risk of CD well into the post-infectious period but the mechanistic basis for this ongoing relationship to disease onset is unknown. We developed two novel models to study the comorbidity of acute gastroenteritis caused by Salmonella Typhimurium or Citrobacter rodentium in mice colonized with adherent-invasive Escherichia coli (AIEC), a bacterial pathobiont linked to CD. Here, we show that disease activity in the post-infectious period after gastroenteritis is driven by the tissue-associated expansion of the resident AIEC pathobiont, with an attendant increase in immunopathology, barrier defects, and delays in mucosal restitution following pathogen clearance. These features required AIEC resistance to host defense peptides and a fulminant inflammatory response to the enteric pathogen. Our results suggest that individuals colonized by AIEC at the time of acute infectious gastroenteritis may be at greater risk for CD onset. Importantly, our data identify AIEC as a tractable disease modifier, a finding that could be exploited in the development of therapeutic interventions following infectious gastroenteritis in at-risk individuals. Western societies have a disproportionately high rate of inflammatory bowel disease (IBD), with growing incidence especially in the adolescent population. A large body of evidence supports the view that bacteria in the gut participate in the pathophysiology of human bowel diseases. The unifying concept is chronic inflammation that is driven by microbial stimulation of the mucosal immune system. However, the mechanisms by which pathogenic or commensal microbes work in concert with each other and with host responses to perpetuate this inflammation is not well known. Adherent-invasive E. coli (AIEC) are Crohn’s disease (CD)-associated bacteria that are implicated in disease pathology. AIEC are pro-inflammatory and may play a central role in maintaining chronic inflammation in response to other CD risk factors, such as acute infectious gastroenteritis. Here, we show that indeed, acute infectious gastroenteritis creates an inflammatory environment in the gut that drives AIEC expansion and worsens disease severity. The increase in disease severity strictly correlates with this AIEC bloom because blocking this bloom by sensitizing AIEC to host defenses also improves the health status of the host. The long time period between recovery from acute gastroenteritis and new onset CD may allow for targeted interventions to mitigate the risk of CD in AIEC-positive individuals.
Collapse
Affiliation(s)
- Cherrie L. Small
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, Canada
| | - Lydia Xing
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, Canada
| | - Joseph B. McPhee
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, Canada
| | - Hong T. Law
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, Canada
| | - Brian K. Coombes
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, Hamilton, Ontario, Canada
- * E-mail:
| |
Collapse
|
56
|
Sartor RB. Review article: the potential mechanisms of action of rifaximin in the management of inflammatory bowel diseases. Aliment Pharmacol Ther 2016; 43 Suppl 1:27-36. [PMID: 26618923 DOI: 10.1111/apt.13436] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 04/27/2015] [Accepted: 08/28/2015] [Indexed: 12/14/2022]
Abstract
BACKGROUND Gut microbiota dysbiosis contributes to the pathogenesis of inflammatory bowel diseases (IBD). Although the microbiota's role in IBD pathogenesis, specifically Crohn's disease (CD), provides a rationale for antibiotic treatment, antibiotic use in CD remains controversial. Rifaximin, traditionally identified as a nonsystemic bactericidal antibiotic, may be therapeutically beneficial for inducing CD remission. AIM To examine the role of rifaximin in the management of IBD and its potential mechanisms of action. METHODS A literature search using the following strategy: ('inflammatory bowel disease' OR 'Crohn's' OR 'ulcerative'), 'rifaximin' AND ('barrier' OR 'translocation' OR 'adhesion' OR 'internalization' OR 'pregnane X'), AND 'pregnane X' AND ('Crohn's' OR 'ulcerative colitis' OR 'inflammatory bowel disease'). RESULTS In vitro data suggest rifaximin mediates changes in epithelial cell physiology and reduces bacterial attachment and internalisation. In experimental colitis models, rifaximin antagonised the effects of tumour necrosis factor-α on intestinal epithelial cells by activating pregnane X receptor, which inhibits nuclear factor-κB-mediated proinflammatory mediators and induces detoxification genes (e.g. multidrug resistance 1 and cytochrome P450 3A4). Rifaximin also inhibits bacterial translocation into the mesenteric lymph nodes. CONCLUSION Accumulating evidence suggests that mechanisms of action of rifaximin in IBD may not be limited to direct bactericidal activity; therefore, rifaximin could potentially be redefined as a gut environment modulator.
Collapse
Affiliation(s)
- R B Sartor
- Center for Gastrointestinal Biology and Disease, Department of Medicine, Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
57
|
Oberc A, Coombes BK. Convergence of External Crohn's Disease Risk Factors on Intestinal Bacteria. Front Immunol 2015; 6:558. [PMID: 26579131 PMCID: PMC4630591 DOI: 10.3389/fimmu.2015.00558] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/19/2015] [Indexed: 01/06/2023] Open
Abstract
Crohn’s disease (CD) is an immune-mediated intestinal illness that significantly compromises health in many developed countries. Although definitive causes remain elusive, the required contribution of microbes in the progression of disease has become an accepted concept. Known CD risk factors, such as antibiotic use and acute infectious gastroenteritis, may impact the gut. This concept is now being explored with a view toward understanding the beneficial and unfavorable microbes that may be altered in numbers during such external insults. A comprehensive understanding of the microbial component to CD could be useful clinically as future therapies may focus on preventing risk exposures on susceptible individuals, eliminating harmful microbes, or restoring a protective gut microbiome. Here, we examine how acute infectious gastroenteritis and antibiotic exposure may impact the gut microbiota in the context of inflammation in CD.
Collapse
Affiliation(s)
- 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 ; Farncombe Family Digestive Health Research Institute , Hamilton, ON , Canada
| |
Collapse
|
58
|
Killing of Escherichia coli by Crohn's Disease Monocyte-derived Macrophages and Its Enhancement by Hydroxychloroquine and Vitamin D. Inflamm Bowel Dis 2015; 21:1499-510. [PMID: 25839777 PMCID: PMC4894789 DOI: 10.1097/mib.0000000000000387] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Crohn's disease (CD) is associated with defective innate immunity, including impaired neutrophil chemotaxis, and mucosal invasion by bacteria, particularly adherent and invasive Escherichia coli that replicate inside macrophage phagolysosomes. We compared CD and healthy control (HC) macrophages for their abilities to kill E. coli and generate neutrophil chemoattractants and also assessed the effects of hydroxychloroquine (HCQ) and vitamin D on killing of phagocytosed E. coli. METHODS Peripheral blood monocyte-derived macrophages from CD and HC were compared for bacterial killing and generation of neutrophil chemoattractants in response to CD-derived E. coli. Escherichia coli replication was also assessed in the presence and absence of HCQ, alone and with antibiotics, and vitamin D. RESULTS Monocyte-derived macrophages from patients with CD were similar to HC in allowing replication of phagocytosed CD-derived E. coli: HM605 {CD: N = 10, mean fold replication in 3 hr = 1.08 (95% confidence interval [CI], 0.39-1.78); HC: N = 9, 1.50 (95% CI, 1.02-1.97); P = 0.15} and also in generation of neutrophil chemoattractants in response to E. coli (mean fold chemotaxis relative to control: CD = 2.55 [95% CI, 2.31-2.80]; HC = 2.65 [95% CI, 2.46-2.85], P = 0.42). HCQ and 1,25 OH2-vitamin D3 both caused dose-dependent inhibition of intramacrophage E. coli replication 3-hour postinfection; HCQ: 73.9% inhibition (P < 0.001) at 1 μg/mL, accompanied by raised intraphagosomal pH, and 1,25 OH2-vitamin D3: 80.7% inhibition (P < 0.05) at 80 nM. HCQ had synergistic effects with doxycycline and ciprofloxacin. CONCLUSIONS CD and HC macrophages perform similarly in allowing replication of phagocytosed E. coli and generating neutrophil chemoattractants. Replication of phagocytosed E. coli was substantially decreased by HCQ and vitamin D. These warrant further therapeutic trials in CD in combination with relevant antibiotics.
Collapse
|
59
|
Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis. PLoS One 2015; 10:e0130902. [PMID: 26125937 PMCID: PMC4509574 DOI: 10.1371/journal.pone.0130902] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/25/2015] [Indexed: 12/30/2022] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strains are detected more frequently within mucosal lesions of patients with Crohn’s disease (CD). The AIEC phenotype consists of adherence and invasion of intestinal epithelial cells and survival within macrophages of these bacteria in vitro. Our aim was to identify candidate transcripts that distinguish AIEC from non-invasive E. coli (NIEC) strains and might be useful for rapid and accurate identification of AIEC by culture-independent technology. We performed comparative RNA-Sequence (RNASeq) analysis using AIEC strain LF82 and NIEC strain HS during exponential and stationary growth. Differential expression analysis of coding sequences (CDS) homologous to both strains demonstrated 224 and 241 genes with increased and decreased expression, respectively, in LF82 relative to HS. Transition metal transport and siderophore metabolism related pathway genes were up-regulated, while glycogen metabolic and oxidation-reduction related pathway genes were down-regulated, in LF82. Chemotaxis related transcripts were up-regulated in LF82 during the exponential phase, but flagellum-dependent motility pathway genes were down-regulated in LF82 during the stationary phase. CDS that mapped only to the LF82 genome accounted for 747 genes. We applied an in silico subtractive genomics approach to identify CDS specific to AIEC by incorporating the genomes of 10 other previously phenotyped NIEC. From this analysis, 166 CDS mapped to the LF82 genome and lacked homology to any of the 11 human NIEC strains. We compared these CDS across 13 AIEC, but none were homologous in each. Four LF82 gene loci belonging to clustered regularly interspaced short palindromic repeats region (CRISPR)—CRISPR-associated (Cas) genes were identified in 4 to 6 AIEC and absent from all non-pathogenic bacteria. As previously reported, AIEC strains were enriched for pdu operon genes. One CDS, encoding an excisionase, was shared by 9 AIEC strains. Reverse transcription quantitative polymerase chain reaction assays for 6 genes were conducted on fecal and ileal RNA samples from 22 inflammatory bowel disease (IBD), and 32 patients without IBD (non-IBD). The expression of Cas loci was detected in a higher proportion of CD than non-IBD fecal and ileal RNA samples (p <0.05). These results support a comparative genomic/transcriptomic approach towards identifying candidate AIEC signature transcripts.
Collapse
|
60
|
da Silva Santos AC, Gomes Romeiro F, Yukie Sassaki L, Rodrigues J. Escherichia coli from Crohn's disease patient displays virulence features of enteroinvasive (EIEC), enterohemorragic (EHEC), and enteroaggregative (EAEC) pathotypes. Gut Pathog 2015; 7:2. [PMID: 25653719 PMCID: PMC4316758 DOI: 10.1186/s13099-015-0050-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/06/2015] [Indexed: 12/28/2022] Open
Abstract
Background Escherichia coli is a normal inhabitant of the gut which upon acquiring virulence factors becomes potentially able to cause diseases. Although E. coli population augments in Crohn’s disease (CD), the reason of this proliferation is not yet clear. CD associated E. coli shows features of extraintestinal pathogenic categories (ExPEC), and eventually the ability to invade cultured epithelial cells, a property observed among diarrheagenic E. coli (DEC). In this work, data on the characterization of an E. coli isolate from a CD patient reveal that, besides invasiveness, CD associated E. coli may harbor other typical DEC markers, namely those defining enterohemorragic (EHEC) and enteroaggregative (EAEC) pathotypes. Results The studied strain, detected both in an ileum biopsy and stools, belonged to the B2 E. coli reference collection (EcoR) phylogroup and harbored the intimin, Shiga cytotoxin 1, and AggR transcriptional activator encoding genes (eae, stx1, aggR, respectively); displayed aggregative adherence to Hep-2 cells and an ability to enter Caco-2 cells four times as high as that of EIEC reference strain and half of invasiveness of AIEC LF82. It was able to enter and replicate in J774 macrophages with invasiveness 85 times as high as that of LF82, but with only one sixth of the intracellular proliferation ability of the later. Extracellular products with cytotoxic activity on Vero cells were detected in strain’s cultures. Preliminary analysis indicated similarity of this strain’s genome with that of O104:H4/2011C-3493. Methods Following its isolation from a resected CD patient, the strain was characterized by in vitro adhesion and invasion assays to Hep-2, invasion to Caco-2 cells and to J774 macrophages and tested for the ability to form biofilm and to produce Shiga cytotoxins. PCRs were carried out to identify virulence genetic markers and for EcoR phylogrouping. The strain’s genome was sequenced by means of Ion torrent PGM platform. Conclusion The detection, in a CD patient, of an E. coli combining virulence features of multiple DEC pathotypes seems not only to stress the relevance of E. coli to CD etiopathogenesis but also to indicate the existence of new and potentially more virulent strains putatively associated with this disease.
Collapse
Affiliation(s)
- Ana Carolina da Silva Santos
- Laboratory of Medical Bacteriology, Department of Microbiology and Immunology, Institute of Biosciences of the State University of São Paulo (UNESP), Brazil, Distrito de Rubião Junior, CEP 18618-970 Botucatu, SP Brazil
| | - Fernando Gomes Romeiro
- Department of Internal Medicine, Botucatu Medical School of the State University of São Paulo (UNESP), Brazil, Distrito de Rubião Junior, CEP 18618-970 Botucatu, SP Brazil
| | - Ligia Yukie Sassaki
- Department of Internal Medicine, Botucatu Medical School of the State University of São Paulo (UNESP), Brazil, Distrito de Rubião Junior, CEP 18618-970 Botucatu, SP Brazil
| | - Josias Rodrigues
- Laboratory of Medical Bacteriology, Department of Microbiology and Immunology, Institute of Biosciences of the State University of São Paulo (UNESP), Brazil, Distrito de Rubião Junior, CEP 18618-970 Botucatu, SP Brazil
| |
Collapse
|
61
|
Understanding host-adherent-invasive Escherichia coli interaction in Crohn's disease: opening up new therapeutic strategies. BIOMED RESEARCH INTERNATIONAL 2014; 2014:567929. [PMID: 25580435 PMCID: PMC4279263 DOI: 10.1155/2014/567929] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/16/2014] [Accepted: 09/16/2014] [Indexed: 02/07/2023]
Abstract
A trillion of microorganisms colonize the mammalian intestine. Most of them have coevolved with the host in a symbiotic relationship and some of them have developed strategies to promote their replication in the presence of competing microbiota. Recent evidence suggests that perturbation of the microbial community favors the emergence of opportunistic pathogens, in particular adherent-invasive Escherichia coli (AIEC) that can increase incidence and severity of gut inflammation in the context of Crohn's disease (CD). This review will report the importance of AIEC as triggers of intestinal inflammation, focusing on their impact on epithelial barrier function and stimulation of mucosal inflammation. Beyond manipulation of immune response, restoration of gut microbiota as a new treatment option for CD patients will be discussed.
Collapse
|
62
|
Martinez-Medina M, Garcia-Gil LJ. Escherichia coli in chronic inflammatory bowel diseases: An update on adherent invasive Escherichia coli pathogenicity. World J Gastrointest Pathophysiol 2014; 5:213-227. [PMID: 25133024 PMCID: PMC4133521 DOI: 10.4291/wjgp.v5.i3.213] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/08/2014] [Accepted: 05/29/2014] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli (E. coli), and particularly the adherent invasive E. coli (AIEC) pathotype, has been increasingly implicated in the ethiopathogenesis of Crohn’s disease (CD). E. coli strains with similar pathogenic features to AIEC have been associated with other intestinal disorders such as ulcerative colitis, colorectal cancer, and coeliac disease, but AIEC prevalence in these diseases remains largely unexplored. Since AIEC was described one decade ago, substantial progress has been made in deciphering its mechanisms of pathogenicity. However, the molecular bases that characterize the phenotypic properties of this pathotype are still not well resolved. A review of studies focused on E. coli populations in inflammatory bowel disease (IBD) is presented here and we discuss about the putative role of this species on each IBD subtype. Given the relevance of AIEC in CD pathogenesis, we present the latest research findings concerning AIEC host-microbe interactions and pathogenicity. We also review the existing data regarding the prevalence and abundance of AIEC in CD and its association with other intestinal diseases from humans and animals, in order to discuss the AIEC disease- and host-specificity. Finally, we highlight the fact that dietary components frequently found in industrialized countries may enhance AIEC colonization in the gut, which merits further investigation and the implementation of preventative measures.
Collapse
|
63
|
Tawfik A, Flanagan PK, Campbell BJ. Escherichia coli-host macrophage interactions in the pathogenesis of inflammatory bowel disease. World J Gastroenterol 2014; 20:8751-8763. [PMID: 25083050 PMCID: PMC4112894 DOI: 10.3748/wjg.v20.i27.8751] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/07/2014] [Accepted: 04/03/2014] [Indexed: 02/06/2023] Open
Abstract
Multiple studies have demonstrated alterations in the intestinal microbial community (termed the microbiome) in Crohn’s disease (CD) and several lines of evidence suggest these changes may have a significant role in disease pathogenesis. In active and quiescent disease, both the faecal and mucosa-associated microbiome are discordant with matched controls with reduced biodiversity, changes in dominant organisms and increased temporal variation described. Mucosa-associated adherent, invasive Escherichia coli (E. coli) (AIEC), pro-inflammatory and resistant to killing by mucosal macrophages, appear to be particularly important. AIEC possess several virulence factors which may confer pathogenic potential in CD. Type-1 pili (FimH) allow adherence to intestinal cells via cell-surface carcinoembryonic antigen-related cell adhesion molecules and possession of long polar fimbrae promotes translocation across the intestinal mucosa via microfold (M)-cells of the follicle-associated epithelium. Resistance to stress genes (htrA, dsbA and hfq) and tolerance of an acidic pH may contribute to survival within the phagolysosomal environment. Here we review the current understanding of the role of mucosa-associated E. coli in Crohn’s pathogenesis, the role of the innate immune system, factors which may contribute to prolonged bacterial survival and therapeutic strategies to target intracellular E. coli.
Collapse
|
64
|
Longman RS, Swaminath A. Microbial manipulation as primary therapy for Crohn's disease. World J Gastroenterol 2013; 19:1513-6. [PMID: 23539531 PMCID: PMC3602467 DOI: 10.3748/wjg.v19.i10.1513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 02/05/2013] [Accepted: 02/07/2013] [Indexed: 02/06/2023] Open
Abstract
While antimicrobials are clinically effective in preventing post-operative recurrence, the role for antibiotics in primary therapy for Crohn’s disease (CD) remains unclear. The recent multicenter phase 2 trial by Prantera et al received wide attention because it demonstrated an increase in the week 12 remission rate in patients with moderately active CD treated with rifaximin and renewed interest in microbial manipulation as primary therapy for CD. In this commentary, we discuss aspects of durability, immune cell polarization, and safety of microbial manipulation as primary therapy for CD.
Collapse
|
65
|
Rifaximin resistance in Escherichia coli associated with inflammatory bowel disease correlates with prior rifaximin use, mutations in rpoB, and activity of Phe-Arg-β-naphthylamide-inhibitable efflux pumps. Antimicrob Agents Chemother 2012. [PMID: 23183443 DOI: 10.1128/aac.02163-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Escherichia coli is implicated in the pathogenesis of inflammatory bowel disease (IBD). Rifaximin, a nonabsorbable derivative of rifampin effective against E. coli, improves symptoms in mild-to-moderate IBD. However, rifaximin resistance can develop in a single step in vitro. We examined the prevalence and mechanisms of rifaximin resistance in 62 strains of E. coli isolated from the ileal mucosa of 50 patients (19 with ileal Crohn's disease [L1+L3], 6 with colonic Crohn's disease [L2], 13 with ulcerative colitis [UC], 4 with symptomatic non-IBD diagnoses [NI], and 8 healthy [H]). Resistance (MIC > 1,024 mg/liter) was present in 12/48 IBD-associated ileal E. coli strains. Resistance correlated with prior rifaximin treatment (P < 0.00000001) but not with the presence of ileal inflammation (P = 0.73) or E. coli phylogroup. Mutations in a 1,057-bp region of rpoB, which encodes the bacterial target of rifaximin, were identified in 10/12 resistant strains versus 0/50 sensitive strains (P < 0.000000001) and consisted of seven amino acid substitutions. The efflux pump inhibitor Phe-Arg-β-naphthylamide (PAβN) lowered the MIC of 9/12 resistant strains 8- to 128-fold. Resistance was stable in the absence of rifaximin in 10/12 resistant strains after 30 passages. We conclude that IBD-associated ileal E. coli frequently manifest resistance to rifaximin that correlates with prior rifaximin use, amino acid substitutions in rpoB, and activity of PAβN-inhibitable efflux pumps, but not with the presence of ileal inflammation or E. coli phylogroup. These findings have significant implications for treatment trials targeting IBD-associated E. coli.
Collapse
|