1
|
Tajuelo A, Carretero O, García-Ríos E, López-Siles M, Cano O, Vázquez M, Más V, Rodríguez-Goncer I, Lalueza A, López-Medrano F, San Juan R, Fernández-Ruiz M, Aguado JM, McConnell MJ, Pérez-Romero P. Corrigendum: Brief Research Report: Virus-Specific Humoral Immunity at Admission Predicts the Development of Respiratory Failure in Unvaccinated SARS-CoV-2 Patients. Front Immunol 2022; 13:965809. [PMID: 35990649 PMCID: PMC9381374 DOI: 10.3389/fimmu.2022.965809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Ana Tajuelo
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Octavio Carretero
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), Madrid, Spain
| | - Estéfani García-Ríos
- Infecciones Víricas e Inmunidad en Enfermos Inmunodeprimidos, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Universidad Internacional de Valencia-VIU, Valencia, Spain
| | - Mireia López-Siles
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Olga Cano
- Biología Viral, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Mónica Vázquez
- Biología Viral, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Vicente Más
- Biología Viral, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Isabel Rodríguez-Goncer
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), Madrid, Spain
| | - Antonio Lalueza
- Department of Internal Medicine, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Francisco López-Medrano
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Department of Medicine, Universidad Complutense, Madrid, Spain
| | - Rafael San Juan
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Department of Medicine, Universidad Complutense, Madrid, Spain
| | - Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Department of Medicine, Universidad Complutense, Madrid, Spain
| | - José M. Aguado
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Department of Medicine, Universidad Complutense, Madrid, Spain
| | - Michael J. McConnell
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pilar Pérez-Romero
- Infecciones Víricas e Inmunidad en Enfermos Inmunodeprimidos, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- *Correspondence: Pilar Pérez-Romero,
| |
Collapse
|
2
|
López-Siles M, McConnell MJ, Martín-Galiano AJ. Identification of Promoter Region Markers Associated With Altered Expression of Resistance-Nodulation-Division Antibiotic Efflux Pumps in Acinetobacter baumannii. Front Microbiol 2022; 13:869208. [PMID: 35663863 PMCID: PMC9161033 DOI: 10.3389/fmicb.2022.869208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic alterations leading to the constitutive upregulation of specific efflux pumps contribute to antibacterial resistance in multidrug resistant bacteria. The identification of such resistance markers remains one of the most challenging tasks of genome-level resistance predictors. In this study, 487 non-redundant genetic events were identified in upstream zones of three operons coding for resistance-nodulation-division (RND) efflux pumps of 4,130 Acinetobacter baumannii isolates. These events included insertion sequences, small indels, and single nucleotide polymorphisms. In some cases, alterations explicitly modified the expression motifs described for these operons, such as the promoter boxes, operators, and Shine-Dalgarno sequences. In addition, changes in DNA curvature and mRNA secondary structures, which are structural elements that regulate expression, were also calculated. According to their influence on RND upregulation, the catalog of upstream modifications were associated with “experimentally verified,” “presumed,” and “probably irrelevant” degrees of certainty. For experimental verification, DNA of upstream sequences independently carrying selected markers, three for each RND operon, were fused to a luciferase reporter plasmid system. Five out of the nine selected markers tested showed significant increases in expression with respect to the wild-type sequence control. In particular, a 25-fold expression increase was observed with the ISAba1 insertion sequence upstream the adeABC pump. Next, overexpression of each of the three multi-specific RND pumps was linked to their respective antibacterial substrates by a deep A. baumannii literature screen. Consequently, a data flow framework was then developed to link genomic upregulatory RND determinants to potential antibiotic resistance. Assignment of potential increases in minimal inhibitory concentrations at the “experimentally verified” level was permitted for 42 isolates to 7–8 unrelated antibacterial agents including tigecycline, which is overlooked by conventional resistome predictors. Thus, our protocol may represent a time-saving filter step prior to laborious confirmation experiments for efflux-driven resistance. Altogether, a computational-experimental pipeline containing all components required for identifying the upstream regulatory resistome is proposed. This schema may provide the foundational stone for the elaboration of tools approaching antibiotic efflux that complement routine resistome predictors for preventing antimicrobial therapy failure against difficult-to-threat bacteria.
Collapse
|
3
|
Tajuelo A, Carretero O, García-Ríos E, López-Siles M, Cano O, Vázquez M, Más V, Rodríguez-Goncer I, Lalueza A, López-Medrano F, Juan RS, Fernández-Ruiz M, Aguado JM, McConnell MJ, Pérez-Romero P. Brief Research Report: Virus-Specific Humoral Immunity at Admission Predicts the Development of Respiratory Failure in Unvaccinated SARS-CoV-2 Patients. Front Immunol 2022; 13:878812. [PMID: 35547738 PMCID: PMC9082065 DOI: 10.3389/fimmu.2022.878812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/29/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction There is robust evidence indicating that the SARS-CoV-2-specific humoral response is associated with protection against severe disease. However, relatively little data exist regarding how the humoral immune response at the time of hospital admission correlates with disease severity in unimmunized patients. Our goal was toidentify variables of the humoral response that could potentially serve as prognostic markers for COVID-19 progressionin unvaccinated SARS-CoV-2 patients. Methods A prospective cross-sectional study was carried out in a cohort of 160 unimmunized, adult COVID-19 patients from the Hospital Universitario 12Octubre. Participants were classified into four clinical groups based on disease severity: non-survivors with respiratory failure (RF), RF survivors, patients requiring oxygen therapy and those not receiving oxygen therapy. Serum samples were taken on admission and IgM, IgG, IgG subclass antibody titers were determined by ELISA, and neutralizing antibody titersusing a surrogate neutralization assay. The differences in the antibody titers between groups and the association between the clinical and analytical characteristics of the patients and the antibody titers were analyzed. Results Patients that developed RF and survived had IgM titers that were 2-fold higher than non-survivors (p = 0.001), higher levels of total IgG than those who developed RF and succumbed to infection (p< 0.001), and than patients who required oxygen therapy (p< 0.05), and had 5-fold higher IgG1 titers than RF non-survivors (p< 0.001) and those who needed oxygen therapy (p< 0.001), and 2-fold higher than patients that did not require oxygen therapy during admission (p< 0.05). In contrast, RF non-survivorshad the lowest neutralizing antibodylevels, which were significantly lower compared those with RF that survived (p = 0.03). A positive correlation was found between IgM, total IgG, IgG1 and IgG3 titers and neutralizing antibody titers in the total cohort (p ≤ 0.0036). Conclusions We demonstrate that patients with RF that survived infection had significantly higher IgM, IgG, IgG1 and neutralizing titers compared to patients with RF that succumb to infection, suggesting that using humoral response variables could be used as a prognostic marker for guiding the clinical management of unimmunized patients admitted to the hospital for SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Ana Tajuelo
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Octavio Carretero
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain
| | - Estéfani García-Ríos
- Infecciones Víricas e Inmunidad en Enfermos Inmunodeprimidos, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Universidad Internacional de Valencia - VIU, Valencia, Spain
| | - Mireia López-Siles
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Olga Cano
- Biología Viral, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Mónica Vázquez
- Biología Viral, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Vicente Más
- Biología Viral, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Isabel Rodríguez-Goncer
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain
| | - Antonio Lalueza
- Department of Internal Medicine, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Francisco López-Medrano
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain
| | - Rafael San Juan
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain
| | - Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain
| | - José Mᵃ Aguado
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain
| | - Michael J McConnell
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pilar Pérez-Romero
- Infecciones Víricas e Inmunidad en Enfermos Inmunodeprimidos, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| |
Collapse
|
4
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| | | |
Collapse
|
5
|
Tajuelo A, López-Siles M, Más V, Pérez-Romero P, Aguado JM, Briz V, McConnell MJ, Martín-Galiano AJ, López D. Cross-Recognition of SARS-CoV-2 B-Cell Epitopes with Other Betacoronavirus Nucleoproteins. Int J Mol Sci 2022; 23:ijms23062977. [PMID: 35328398 PMCID: PMC8955325 DOI: 10.3390/ijms23062977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/08/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
The B and T lymphocytes of the adaptive immune system are important for the control of most viral infections, including COVID-19. Identification of epitopes recognized by these cells is fundamental for understanding how the immune system detects and removes pathogens, and for antiviral vaccine design. Intriguingly, several cross-reactive T lymphocyte epitopes from SARS-CoV-2 with other betacoronaviruses responsible for the common cold have been identified. In addition, antibodies that cross-recognize the spike protein, but not the nucleoprotein (N protein), from different betacoronavirus have also been reported. Using a consensus of eight bioinformatic methods for predicting B-cell epitopes and the collection of experimentally detected epitopes for SARS-CoV and SARS-CoV-2, we identified four surface-exposed, conserved, and hypothetical antigenic regions that are exclusive of the N protein. These regions were analyzed using ELISA assays with two cohorts: SARS-CoV-2 infected patients and pre-COVID-19 samples. Here we describe four epitopes from SARS-CoV-2 N protein that are recognized by the humoral response from multiple individuals infected with COVID-19, and are conserved in other human coronaviruses. Three of these linear surface-exposed sequences and their peptide homologs in SARS-CoV-2 and HCoV-OC43 were also recognized by antibodies from pre-COVID-19 serum samples, indicating cross-reactivity of antibodies against coronavirus N proteins. Different conserved human coronaviruses (HCoVs) cross-reactive B epitopes against SARS-CoV-2 N protein are detected in a significant fraction of individuals not exposed to this pandemic virus. These results have potential clinical implications.
Collapse
Affiliation(s)
- Ana Tajuelo
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Mireia López-Siles
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Vicente Más
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Pilar Pérez-Romero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | | | - Verónica Briz
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Michael J. McConnell
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
- Correspondence: (M.J.M.); (D.L.)
| | - Antonio J. Martín-Galiano
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
| | - Daniel López
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain; (A.T.); (M.L.-S.); (V.M.); (P.P.-R.); (V.B.); (A.J.M.-G.)
- Correspondence: (M.J.M.); (D.L.)
| |
Collapse
|
6
|
Prieto Martin Gil S, Tajuelo A, López-Siles M, McConnell MJ. Subinhibitory Concentrations of Clinically-Relevant Antimicrobials Affect Resistance-Nodulation-Division Family Promoter Activity in Acinetobacter baumannii. Front Microbiol 2021; 12:780201. [PMID: 34925284 PMCID: PMC8678518 DOI: 10.3389/fmicb.2021.780201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/11/2021] [Indexed: 11/26/2022] Open
Abstract
Efflux pumps contribute to multidrug resistance in Acinetobacter baumannii due to their ability to expel a wide variety of structurally unrelated compounds. This study aimed to characterize the effect of subinhibitory concentrations of clinically-relevant antibiotics and disinfectants on the promoter activity of members of the Resistance-Nodulation-Division (RND) family in A. baumannii. The promoter regions from three RND efflux pumps (AdeABC, AdeFGH and AdeIJK) and the AdeRS regulatory system from three different A. baumannii strains (ATCC 17961, ATCC 17978, and ATCC 19606) were cloned into a luciferase reporter system (pLPV1Z). Promoter activity was quantitatively assessed in both exponential and stationary phase cultures after exposure to subinhibitory concentrations of four antibiotics from different classes (rifampicin, meropenem, tigecycline and colistin) and two disinfectants (ethanol and chlorhexidine). Subinhibitory concentrations of the compounds tested had variable effects on promoter activity that were highly dependent on the A. baumannii strain, the compound tested and the growth phase. Fold changes in AdeABC promoter activity ranged from 1.97 to 113.7, in AdeFGH from −5.6 to 1.13, in AdeIJK from −2.5 to 2, and in AdeRS from −36.2 to −1.32. Taken together, these results indicate that subinhibitory concentrations of clinically-relevant antibiotics and disinfectants affect the promoter activity of RND family members in A. baumannii in a strain and growth phase dependent manner. These results may have important implications for the treatment of infections caused by A. baumannii.
Collapse
Affiliation(s)
- Sonia Prieto Martin Gil
- Intrahospital Infections Laboratory, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Ana Tajuelo
- Intrahospital Infections Laboratory, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Mireia López-Siles
- Intrahospital Infections Laboratory, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Michael J McConnell
- Intrahospital Infections Laboratory, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| |
Collapse
|
7
|
García-Ríos E, Gata-de-Benito J, López-Siles M, McConnell MJ, Pérez-Romero P. Optimization of a Lambda-RED Recombination Method for Rapid Gene Deletion in Human Cytomegalovirus. Int J Mol Sci 2021; 22:10558. [PMID: 34638896 DOI: 10.3390/ijms221910558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022] Open
Abstract
Human cytomegalovirus (HCMV) continues to be a major cause of morbidity in transplant patients and newborns. However, the functions of many of the more than 282 genes encoded in the HCMV genome remain unknown. The development of bacterial artificial chromosome (BAC) technology contributes to the genetic manipulation of several organisms including HCMV. The maintenance of the HCMV BAC in E. coli cells permits the rapid generation of recombinant viral genomes that can be used to produce viral progeny in cell cultures for the study of gene function. We optimized the Lambda-Red Recombination system to construct HCMV gene deletion mutants rapidly in the complete set of tested genes. This method constitutes a useful tool that allows for the quick generation of a high number of gene deletion mutants, allowing for the analysis of the whole genome to improve our understanding of HCMV gene function. This may also facilitate the development of novel vaccines and therapeutics.
Collapse
|
8
|
López-Siles M, Corral-Lugo A, McConnell MJ. Vaccines for multidrug resistant Gram negative bacteria: lessons from the past for guiding future success. FEMS Microbiol Rev 2021; 45:fuaa054. [PMID: 33289833 DOI: 10.1093/femsre/fuaa054] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance is a major threat to global public health. Vaccination is an effective approach for preventing bacterial infections, however it has not been successfully applied to infections caused by some of the most problematic multidrug resistant pathogens. In this review, the potential for vaccines to contribute to reducing the burden of disease of infections caused by multidrug resistant Gram negative bacteria is presented. Technical, logistical and societal hurdles that have limited successful vaccine development for these infections in the past are identified, and recent advances that can contribute to overcoming these challenges are assessed. A synthesis of vaccine technologies that have been employed in the development of vaccines for key multidrug resistant Gram negative bacteria is included, and emerging technologies that may contribute to future successes are discussed. Finally, a comprehensive review of vaccine development efforts over the last 40 years for three of the most worrisome multidrug resistant Gram negative pathogens, Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa is presented, with a focus on recent and ongoing studies. Finally, future directions for the vaccine development field are highlighted.
Collapse
Affiliation(s)
- Mireia López-Siles
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Andrés Corral-Lugo
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Michael J McConnell
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| |
Collapse
|
9
|
Corral-Lugo A, López-Siles M, López D, McConnell MJ, Martin-Galiano AJ. Identification and Analysis of Unstructured, Linear B-Cell Epitopes in SARS-CoV-2 Virion Proteins for Vaccine Development. Vaccines (Basel) 2020; 8:E397. [PMID: 32698423 DOI: 10.3390/vaccines8030397] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 12/13/2022] Open
Abstract
The efficacy of SARS-CoV-2 nucleic acid-based vaccines may be limited by proteolysis of the translated product due to anomalous protein folding. This may be the case for vaccines employing linear SARS-CoV-2 B-cell epitopes identified in previous studies since most of them participate in secondary structure formation. In contrast, we have employed a consensus of predictors for epitopic zones plus a structural filter for identifying 20 unstructured B-cell epitope-containing loops (uBCELs) in S, M, and N proteins. Phylogenetic comparison suggests epitope switching with respect to SARS-CoV in some of the identified uBCELs. Such events may be associated with the reported lack of serum cross-protection between the 2003 and 2019 pandemic strains. Incipient variability within a sample of 1639 SARS-CoV-2 isolates was also detected for 10 uBCELs which could cause vaccine failure. Intermediate stages of the putative epitope switch events were observed in bat coronaviruses in which additive mutational processes possibly facilitating evasion of the bat immune system appear to have taken place prior to transfer to humans. While there was some overlap between uBCELs and previously validated SARS-CoV B-cell epitopes, multiple uBCELs had not been identified in prior studies. Overall, these uBCELs may facilitate the development of biomedical products for SARS-CoV-2.
Collapse
|
10
|
Lopez-Siles M, Aldeguer X, Sabat-Mir M, Serra-Pagès M, Duncan SH, Flint HJ, Garcia-Gil LJ, Martinez-Medina M. Evaluation of bacterial biomarkers to aid in challenging inflammatory bowel diseases diagnostics and subtype classification. World J Gastrointest Pathophysiol 2020; 11:64-77. [PMID: 32435523 PMCID: PMC7226914 DOI: 10.4291/wjgp.v11.i3.64] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/27/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The challenges for inflammatory bowel disease (IBD) diagnostics are to discriminate it from gut conditions with similar symptoms such as irritable bowel syndrome (IBS), to distinguish IBD subtypes, to predict disease progression, and to establish the risk to develop colorectal cancer (CRC). Alterations in gut microbiota have been proposed as a source of information to assist in IBD diagnostics. Faecalibacterium prausnitzii (F. prausnitzii), its phylogroups, and Escherichia coli (E. coli) have been reported as potential biomarkers, but their performance in challenging IBD diagnostic situations remains elusive. We hypothesize that bacterial biomarkers based in these species may help to discriminate these conditions of complex diagnostics.
AIM To evaluate the usefulness of indices calculated from the quantification of these species as biomarkers to aid in IBD diagnostics.
METHODS A retrospective study of 131 subjects (31 controls (H); 45 Crohn’s disease (CD), 25 ulcerative colitis (UC), 10 IBS, and 20 CRC patients) was performed to assess the usefulness of bacterial biomarkers in biopsies. Further, the performance of biomarkers in faeces was studied in 29 stool samples (19 CD, 10 UC). Relative abundances of total F. prausnitzii (FP), its phylogroups (PHGI and PHGII), and E. coli (E) quantification were determined by qPCR. Loads were combined to calculate the FP-E index, the PHGI–E index and the PHGII-E index. Biomarkers accuracy to discriminate among conditions was measured by the area under the receiver operating characteristic curve (AUC).
RESULTS In biopsies, FP-E index was good for discriminating IBS from CD (AUC = 0.752) while PHGII-E index was suitable for discriminating IBS from UC (AUC = 0.632). The FP-E index would be the choice to discriminate IBD from CRC, especially from all UC subtypes (AUC ≥ 0.875), regardless of the activity status of the patient. Discrimination between UC patients that had the longest disease duration and those with CRC featured slightly lower AUC values. Concerning differentiation in IBD with shared location, PHGI-E index can establish progression from proctitis and left-sided colitis to ulcerative pancolitis (AUC ≥ 0.800). PHG I-E index analysis in tissue would be the choice to discriminate within IBD subtypes of shared location (AUC ≥ 0.712), while in non-invasive faecal samples FP or PHGI could be good indicators (AUC ≥ 0.833).
CONCLUSION F. prausnitzii phylogroups combined with E. coli offer potential to discriminate between IBD and CRC patients and can assist in IBD subtypes classification, which may help in solving IBD diagnostics challenges.
Collapse
Affiliation(s)
- Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona 17003, Spain
| | - Xavier Aldeguer
- Department of Gastroenterology, Hospital Universitari Dr. Josep Trueta, Girona 17007, Spain
| | - Miriam Sabat-Mir
- Department of Gastroenterology, Hospital Santa Caterina, Salt 17190, Spain
| | | | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
| | - L Jesús Garcia-Gil
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona 17003, Spain
| | - Margarita Martinez-Medina
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona 17003, Spain
| |
Collapse
|
11
|
Fassatoui M, Lopez-Siles M, Díaz-Rizzolo DA, Jmel H, Naouali C, Abdessalem G, Chikhaoui A, Nadal B, Jamoussi H, Abid A, Gomis R, Abdelhak S, Martinez-Medina M, Kefi R. Gut microbiota imbalances in Tunisian participants with type 1 and type 2 diabetes mellitus. Biosci Rep 2019; 39:BSR20182348. [PMID: 31147456 PMCID: PMC6579978 DOI: 10.1042/bsr20182348] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/22/2022] Open
Abstract
Gut microbiota plays an important role in the regulation of the immune system and host's metabolism. We aimed to characterize the gut microbiota of Tunisian participants with and without diabetes.We enrolled ten participants with type 1 diabetes mellitus (T1DM), ten patients with type 2 diabetes mellitus (T2DM), and 11 subjects without diabetes. Bacteria was quantified in fecal samples by quantitative PCR (qPCR). Statistical tests and multivariate analysis were performed using RStudio program.Results showed that the proportions of Firmicutes, Akkermansia muciniphila, and Faecalibacterium prausnitzii (P≤0.041), as well as, the ratio Firmicutes/Bacteroidetes decreased in participants with T1DM compared with those without diabetes (p = 0.036). Participants with T2DM presented a reduction in the amounts of A. muciniphila and F. prausnitzii compared with those without diabetes (P≤0.036). Furthermore, A. muciniphila is negatively correlated with glucose level (P=0.022) and glycated hemoglobin (HbA1c) (P=0.035). Multivariate analysis revealed that participants with diabetes formed a cluster apart compared with those without diabetes.In conclusion the gut bacteria of Tunisian participants with diabetes was altered. The gut bacterial profile, especially the distribution of A muciniphila in participants with diabetes was affected by glycemic dysregulation. The investigation of the gut microbiota may help clinicians to improve diagnosis and treatment of diabetes and its complications.
Collapse
Affiliation(s)
- Meriem Fassatoui
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
| | - Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Maria Aurèlia Capmany, 40, 17003, Girona, Spain
| | - Diana A Díaz-Rizzolo
- Diabetes and Obesity Research Laboratory, Institut d'Investigations Biomèdiques, August Pi I Sunyer (IDIBAPS), Hospital Clinic, Rosselló 149-153, 08036, Barcelona Spain
| | - Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
| | - Chokri Naouali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
| | - Ghaith Abdessalem
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
| | - Asma Chikhaoui
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
| | - Belén Nadal
- Diabetes and Obesity Research Laboratory, Institut d'Investigations Biomèdiques, August Pi I Sunyer (IDIBAPS), Hospital Clinic, Rosselló 149-153, 08036, Barcelona Spain
| | - Henda Jamoussi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- Department of Nutritional Diseases A, National Institute of Nutrition and Food Technology, 11, Rue Djebel Lakhdar, Bab Saâdoun, 1007, Tunis, Tunisia
| | - Abdelmajid Abid
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- Department of External Consultation, National Institute of Nutrition and Food Technology, 11, Rue Djebel Lakhdar, Bab Saâdoun, 1007, Tunis, Tunisia
| | - Ramon Gomis
- Diabetes and Obesity Research Laboratory, Institut d'Investigations Biomèdiques, August Pi I Sunyer (IDIBAPS), Hospital Clinic, Rosselló 149-153, 08036, Barcelona Spain
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
| | - Margarita Martinez-Medina
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Maria Aurèlia Capmany, 40, 17003, Girona, Spain
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, 13, Place Pasteur, B.P.74, 1002, Belvédère, Tunis, Tunisia
- University of Tunis El Manar, Campus Universitaire Farhat Hached, BP n° 94, Rommana, 1068, Tunis, Tunisia
| |
Collapse
|
12
|
Díaz-Rizzolo DA, Kostov B, López-Siles M, Serra A, Colungo C, González-de-Paz L, Martinez-Medina M, Sisó-Almirall A, Gomis R. Healthy dietary pattern and their corresponding gut microbiota profile are linked to a lower risk of type 2 diabetes, independent of the presence of obesity. Clin Nutr 2019; 39:524-532. [PMID: 30876826 DOI: 10.1016/j.clnu.2019.02.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 02/21/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Prediabetes and old age are both high risk factors for developing Type 2 Diabetes (T2D), while obesity is one of the most important factors triggering the disease. Nutritional interventions are the most effective tool for preventing T2D, as they improve different biochemical and anthropometric outcomes and growth-promoting/inhibiting gut microbiota populations. However, to date there are no specific dietary recommendations to stop the development of T2D in elderly groups, for whom hypocaloric diets and other commonly used weight-loss programs could be considered dangerous. The objective of our study, thus, was to understand the impact of dietary patterns on T2D risk as related to gut microbiota profile in obese and non-obese elderly prediabetic subjects. METHODS A cross-sectional study was performed in 182 subjects ≥65 years old with prediabetes, divided into obese (OB) or non-obese (NOB) subgroups, and their risk of developing T2D was measured according to FINDRISK score and biochemical parameters. Also, clusters into different dietary patterns in each group by PCA analysis was related with gut microbiota, which was analyzed from stool samples by qPCR. The creation of clusters was used to re-evaluate T2D risk. RESULTS OB was at higher risk of developing T2D and showed worse metabolic outcomes. Unhealthier and healthier dietary pattern clusters were observed for both OB (OB-6 and OB-5 respectively) and NOB (NOB-2 and NOB-3 respectively) groups. Results obtained from the gut microbiota showed that only Prevotella was higher in NOB, but when comparisons were made between clusters, a clear relation with dietary pattern was observed; showing in healthier dietary clusters a decrease in Prevotella, an increase of Faecalibacterium prausnitzii and an increase in lactic acid bacteria. T2D risk was greater in the obese group between unhealthier dietary clusters. No difference between healthier dietary clusters was observed. CONCLUSION A healthy dietary pattern and the growth-promoting beneficial and growth-inhibiting disadvantageous gut microbiota populations linked to it provide protection against the development of T2D in an obese population with advanced age and preDM.
Collapse
Affiliation(s)
- D A Díaz-Rizzolo
- Diabetes and Obesity Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clinic of Barcelona, Barcelona, Spain
| | - B Kostov
- Primary Care Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Primary Care Centre Les Corts, CAPSBE, Barcelona, Spain
| | - M López-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - A Serra
- Diabetes and Obesity Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clinic of Barcelona, Barcelona, Spain
| | - C Colungo
- Primary Care Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Primary Care Centre Les Corts, CAPSBE, Barcelona, Spain
| | - L González-de-Paz
- Primary Care Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Primary Care Centre Les Corts, CAPSBE, Barcelona, Spain
| | - M Martinez-Medina
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - A Sisó-Almirall
- Primary Care Research Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Primary Care Centre Les Corts, CAPSBE, Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - R Gomis
- Diabetes and Obesity Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clinic of Barcelona, Barcelona, Spain; University of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Spain; Department of Endocrinology and Nutrition, Hospital Clinic of Barcelona, Barcelona, Spain; Faculty of Health Sciences, Universitat Oberta de Catalunya, Barcelona, Spain.
| |
Collapse
|
13
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| | | |
Collapse
|
14
|
Lopez-Siles M, Enrich-Capó N, Aldeguer X, Sabat-Mir M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects. Front Cell Infect Microbiol 2018; 8:281. [PMID: 30245977 PMCID: PMC6137959 DOI: 10.3389/fcimb.2018.00281] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 07/25/2018] [Indexed: 12/21/2022] Open
Abstract
Akkermansia muciniphila and Faecalibacterium prausnitzii, cohabitants in the intestinal mucosa, are considered members of a healthy microbiota and reduction of both species occurs in several intestinal disorders, including inflammatory bowel disease. Little is known however about a possible link between the reduction in quantity of these species, and in which circumstances this may occur. This study aims to determine the abundances and co-occurrence of the two species in order to elucidate conditions that may compromise their presence in the gut. Loads of A. muciniphila, total F. prausnitzii and its two phylogroup (16S rRNA gene copies) were determined by quantitative polymerase chain reaction in colonic biopsies from 17 healthy controls (H), 23 patients with ulcerative colitis (UC), 31 patients with Crohn's disease (CD), 3 with irritable bowel syndrome (IBS) and 3 with colorectal cancer (CRC). Data were normalized to total bacterial 16S rRNA gene copies in the same sample. Prevalence, relative abundances and correlation analyses were performed according to type of disease and considering relevant clinical characteristics of patients such as IBD location, age of disease onset, CD behavior, current medication and activity status. Co-occurrence of both species was found in 29% of H, 65% of UC and 29% of CD. Lower levels of total F. prausnitzii and phylogroups were found in subjects with CD, compared with H subjects (P ≤ 0.044). In contrast, no differences were found with the regard to A. muciniphila abundance across different disease states, but CD patients with disease onset below 16 years of age featured a marked depletion of this species. In CD patients, correlation between A. muciniphila and total F. prausnitzii (ρ = 0.362, P = 0.045) was observed, and particularly in those with non-stricturing, non-penetrating disease behavior and under moderate immunosuppressants therapy. Altogether, this study revealed that co-occurrence of both species differs between disease status. In addition, IBD patients featured a reduction of F. prausnitzii but similar loads of A. muciniphila when compared to H subjects, with the exception of those with early onset CD. Depletion of A. muciniphila in this subgroup of subjects suggests that it could be a potential biomarker to assist in pediatric CD diagnosis.
Collapse
Affiliation(s)
- Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Núria Enrich-Capó
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Xavier Aldeguer
- Department of Gastroenterology, Hospital Dr. Josep Trueta, Girona, Spain
| | - Miriam Sabat-Mir
- Department of Gastroenterology, Hospital Santa Caterina, Girona, Spain
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, Aberdeen, United Kingdom
| | - L Jesús Garcia-Gil
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | | |
Collapse
|
15
|
Camprubí-Font C, Lopez-Siles M, Ferrer-Guixeras M, Niubó-Carulla L, Abellà-Ametller C, Garcia-Gil LJ, Martinez-Medina M. Comparative genomics reveals new single-nucleotide polymorphisms that can assist in identification of adherent-invasive Escherichia coli. Sci Rep 2018; 8:2695. [PMID: 29426864 DOI: 10.1038/s41598-018-20843-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [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.
Collapse
|
16
|
Lopez-Siles M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. ISME J 2017; 11:841-852. [PMID: 28045459 PMCID: PMC5364359 DOI: 10.1038/ismej.2016.176] [Citation(s) in RCA: 403] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/15/2016] [Accepted: 11/10/2016] [Indexed: 12/13/2022]
Abstract
There is an increasing interest in Faecalibacterium prausnitzii, one of the most abundant bacterial species found in the gut, given its potentially important role in promoting gut health. Although some studies have phenotypically characterized strains of this species, it remains a challenge to determine which factors have a key role in maintaining the abundance of this bacterium in the gut. Besides, phylogenetic analysis has shown that at least two different F. prausnitzii phylogroups can be found within this species and their distribution is different between healthy subjects and patients with gut disorders. It also remains unknown whether or not there are other phylogroups within this species, and also if other Faecalibacterium species exist. Finally, many studies have shown that F. prausnitzii abundance is reduced in different intestinal disorders. It has been proposed that F. prausnitzii monitoring may therefore serve as biomarker to assist in gut diseases diagnostics. In this mini-review, we aim to serve as an overview of F. prausnitzii phylogeny, ecophysiology and diversity. In addition, strategies to modulate the abundance of F. prausnitzii in the gut as well as its application as a biomarker for diagnostics and prognostics of gut diseases are discussed. This species may be a useful potential biomarker to assist in ulcerative colitis and Crohn's disease discrimination.
Collapse
Affiliation(s)
- Mireia Lopez-Siles
- Laboratori de Microbiologia Molecular, Departament de Biologia, Universitat de Girona, Girona, Spain
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - L Jesús Garcia-Gil
- Laboratori de Microbiologia Molecular, Departament de Biologia, Universitat de Girona, Girona, Spain
- Laboratori de Microbiologia Molecular, Departament de Biologia, Universitat de Girona, Carrer de Maria Aurèlia Capmany, 40, E-17003, Girona, Spain. E-mail:
| | - Margarita Martinez-Medina
- Laboratori de Microbiologia Molecular, Departament de Biologia, Universitat de Girona, Girona, Spain
| |
Collapse
|
17
|
Lopez-Siles M, Martinez-Medina M, Surís-Valls R, Aldeguer X, Sabat-Mir M, Duncan SH, Flint HJ, Garcia-Gil LJ. Changes in the Abundance of Faecalibacterium prausnitzii Phylogroups I and II in the Intestinal Mucosa of Inflammatory Bowel Disease and Patients with Colorectal Cancer. Inflamm Bowel Dis 2016; 22:28-41. [PMID: 26595550 DOI: 10.1097/MIB.0000000000000590] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Faecalibacterium prausnitzii comprises 2 phylogroups, whose abundance in healthy and diseased gut and in conjunction with Escherichia coli has not yet been studied. This work aims to determine the contribution of F. prausnitzii phylogroups I and II in intestinal disease and to assess their potential diagnostic usefulness as biomarkers for gut diseases. METHODS Total F. prausnitzii, its phylogroups, and E. coli loads were determined by quantitative polymerase chain reaction targeting the 16S rRNA gene on biopsies from 31 healthy controls (H), 45 patients with Crohn's disease (CD), 25 patients with ulcerative colitis, 10 patients with irritable bowel syndrome, and 20 patients with colorectal cancer. Data were normalized to total bacterial counts and analyzed according to patients' disease location and clinical characteristics. RESULTS Lower levels of both total F. prausnitzii and phylogroup I were found in subjects with CD, ulcerative colitis, and colorectal cancer (P < 0.001) compared with H subjects. Phylogroup I load was a better biomarker than total F. prausnitzii to discriminate subjects with gut disorders from H. Phylogroup II depletion was observed only in patients with CD (P < 0.001) and can be potentially applied to differentiate ulcerative pancolitis from colonic CD. No statistically significant correlation between E. coli and any of the 2 F. prausnitzii phylogroups was found in any group of patients or by inflammatory bowel disease location. Phylogroup I was lower in active patients with CD, whereas those CD with intestinal resection showed a reduction in phylogroup II. Treatments with mesalazine and immunosuppressants did not result in the recovery of F. prausnitzii phylogroups abundance. CONCLUSIONS F. prausnitzii phylogroup I was depleted in CD, ulcerative colitis, and colorectal cancer, whereas phylogroup II was specifically reduced in CD. Quantification of F. prausnitzii phylogroups and E. coli may help to identify gut disorders and to classify inflammatory bowel disease location.
Collapse
|
18
|
Busquets D, Mas-de-Xaxars T, López-Siles M, Martínez-Medina M, Bahí A, Sàbat M, Louvriex R, Miquel-Cusachs JO, Garcia-Gil JL, Aldeguer X. Anti-tumour Necrosis Factor Treatment with Adalimumab Induces Changes in the Microbiota of Crohn's Disease. J Crohns Colitis 2015; 9:899-906. [PMID: 26142465 DOI: 10.1093/ecco-jcc/jjv119] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 06/30/2015] [Indexed: 12/29/2022]
Abstract
BACKGROUND The composition of the intestinal microbiota is altered in Crohn's disease [CD] patients. The objective of this study was to evaluate the qualitative and quantitative changes in the microbiota of CD patients in 3 months of treatment with adalimumab [ADA], and determine whether or not these changes are produced towards the recovery of the normal, healthy-like microbiota. METHODS The microbiota composition, and the Faecalibacterium prausnitzii / Escherichia coli quantitative relationship as dysbiosis indicator, were studied at baseline [T0], one month [T1], and 3 months [T3] after starting treatment using a polymerase chain reaction-denaturing gradient gel electrophoresis [PCR-DGGE] of 16S rRNA gene fragments and quantitative PCR, respectively, in rectal mucosal biopsies from 15 CD patients and four healthy subjects. RESULTS T0 and T3 fingerprints were different in all patients; whereas T1 and T3 presented similar patterns. Recovered phylogroups were Firmicutes [79.1%], Bacteroides [12.5%], and Actinobacteria [6.25%]. The prevalence of E. coli decreased during treatment. Relative E. coli loads in CD samples were significantly reduced at every analysed step [T1 and T3] [p < 0.005] whereas no significant changes were observed in relative F. prausnitzii counts. CONCLUSION Treatment with ADA induces short-term changes in the microbiota composition which seem to parallel the partial recovery of the gut bacterial ecology, with recovery parameters tending to eubiosis recovery. The quantitative determination of dysbiosis-representative bacteria, such as E. coli, may provide a fast and reliable indicator of the healing state of the intestinal mucosa.
Collapse
Affiliation(s)
- David Busquets
- Department of Gastroenterology, Hospital Dr. Josep Trueta, Girona, Catalonia, Spain
| | - Teresa Mas-de-Xaxars
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Catalonia, Spain
| | - Mireia López-Siles
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Catalonia, Spain
| | | | - Anna Bahí
- Department of Gastroenterology, Hospital Dr. Josep Trueta, Girona, Catalonia, Spain
| | - Miriam Sàbat
- Gastroenterology Unit, Hospital Santa Caterina, Girona, Catalonia, Spain
| | - René Louvriex
- Department of Gastroenterology, Hospital Dr. Josep Trueta, Girona, Catalonia, Spain
| | | | - Jesus L Garcia-Gil
- Laboratory of Molecular Microbiology, Department of Biology, University of Girona, Catalonia, Spain
| | - Xavier Aldeguer
- Department of Gastroenterology, Hospital Dr. Josep Trueta, Girona, Catalonia, Spain
| |
Collapse
|
19
|
Lopez-Siles M, Martinez-Medina M, Abellà C, Busquets D, Sabat-Mir M, Duncan SH, Aldeguer X, Flint HJ, Garcia-Gil LJ. Mucosa-associated Faecalibacterium prausnitzii phylotype richness is reduced in patients with inflammatory bowel disease. Appl Environ Microbiol 2015; 81:7582-92. [PMID: 26296733 DOI: 10.1128/AEM.02006-15] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/18/2015] [Indexed: 12/11/2022] Open
Abstract
Faecalibacterium prausnitzii depletion in intestinal diseases has been extensively reported, but little is known about intraspecies variability. This work aims to determine if subjects with gastrointestinal disease host mucosa-associated F. prausnitzii populations different from those hosted by healthy individuals. A new species-specific PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method targeting the 16S rRNA gene was developed to fingerprint F. prausnitzii populations in biopsy specimens from 31 healthy control (H) subjects and 36 Crohn's disease (CD), 23 ulcerative colitis (UC), 6 irritable bowel syndrome (IBS), and 22 colorectal cancer (CRC) patients. The richness of F. prausnitzii subtypes was lower in inflammatory bowel disease (IBD) patients than in H subjects. The most prevalent operational taxonomic units (OTUs) consisted of four phylotypes (OTUs with a 99% 16S rRNA gene sequence similarity [OTU99]), which were shared by all groups of patients. Their distribution and the presence of some disease-specific F. prausnitzii phylotypes allowed us to differentiate the populations in IBD and CRC patients from that in H subjects. At the level of a minimum similarity of 97% (OTU97), two phylogroups accounted for 98% of the sequences. Phylogroup I was found in 87% of H subjects but in under 50% of IBD patients (P = 0.003). In contrast, phylogroup II was detected in >75% of IBD patients and in only 52% of H subjects (P = 0.005). This study reveals that even though the main members of the F. prausnitzii population are present in both H subjects and individuals with gut diseases, richness is reduced in the latter and an altered phylotype distribution exists between diseases. This approach may serve as a basis for addressing the suitability of F. prausnitzii phylotypes to be quantified as a putative biomarker of disease and depicting the importance of the loss of these subtypes in disease pathogenesis.
Collapse
|
20
|
Lopez-Siles M, Martinez-Medina M, Busquets D, Sabat-Mir M, Duncan SH, Flint HJ, Aldeguer X, Garcia-Gil LJ. Mucosa-associated Faecalibacterium prausnitzii and Escherichia coli co-abundance can distinguish Irritable Bowel Syndrome and Inflammatory Bowel Disease phenotypes. Int J Med Microbiol 2014; 304:464-75. [PMID: 24713205 DOI: 10.1016/j.ijmm.2014.02.009] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/31/2013] [Accepted: 02/09/2014] [Indexed: 12/19/2022] Open
Affiliation(s)
- Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | | | - David Busquets
- Departament de Gastroenterologia, Hospital Dr. Josep Trueta, Girona, Spain
| | - Miriam Sabat-Mir
- Departament de Gastroenterologia, Hospital Santa Caterina, Salt, Girona, Spain
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Harry J Flint
- Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Xavier Aldeguer
- Departament de Gastroenterologia, Hospital Dr. Josep Trueta, Girona, Spain
| | - L Jesús Garcia-Gil
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain.
| |
Collapse
|
21
|
Soler M, Ruiz-Rueda O, Lopez-Siles M, Calvó L, Kaclíková E, García-Gil JL. A validated simple and rapid method for the simultaneous detection of both Cronobacter spp. and Salmonella spp. for infant formula quality control. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s13594-011-0054-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
22
|
Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJ, Garcia-Gil LJ, Flint HJ. Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl Environ Microbiol 2012; 78:420-8. [PMID: 22101049 DOI: 10.1128/AEM.06858-11] [Citation(s) in RCA: 278] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Faecalibacterium prausnitzii is one of the most abundant commensal bacteria in the healthy human large intestine, but information on genetic diversity and substrate utilization is limited. Here, we examine the phylogeny, phenotypic characteristics, and influence of gut environmental factors on growth of F. prausnitzii strains isolated from healthy subjects. Phylogenetic analysis based on the 16S rRNA sequences indicated that the cultured strains were representative of F. prausnitzii sequences detected by direct analysis of fecal DNA and separated the available isolates into two phylogroups. Most F. prausnitzii strains tested grew well under anaerobic conditions on apple pectin. Furthermore, F. prausnitzii strains competed successfully in coculture with two other abundant pectin-utilizing species, Bacteroides thetaiotaomicron and Eubacterium eligens, with apple pectin as substrate, suggesting that this species makes a contribution to pectin fermentation in the colon. Many F. prausnitzii isolates were able to utilize uronic acids for growth, an ability previously thought to be confined to Bacteroides spp. among human colonic anaerobes. Most strains grew on N-acetylglucosamine, demonstrating an ability to utilize host-derived substrates. All strains tested were bile sensitive, showing at least 80% growth inhibition in the presence of 0.5 μg/ml bile salts, while inhibition at mildly acidic pH was strain dependent. These attributes help to explain the abundance of F. prausnitzii in the colonic community but also suggest factors in the gut environment that may limit its distribution.
Collapse
|
23
|
Soler M, Ruiz-rueda O, Lopez-siles M, Calvó L, Kaclíková E, García-gil JL. A New Validated Real-Time PCR-Based Method for the Specific and Fast Detection of Cronobacter spp. in Infant Formula. FOOD ANAL METHOD 2012; 5:179-87. [DOI: 10.1007/s12161-011-9252-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
24
|
Martinez-Medina M, Aldeguer X, Lopez-Siles M, González-Huix F, López-Oliu C, Dahbi G, Blanco JE, Blanco J, Garcia-Gil LJ, Darfeuille-Michaud A. Molecular diversity of Escherichia coli in the human gut: new ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohn's disease. Inflamm Bowel Dis 2009; 15:872-82. [PMID: 19235912 DOI: 10.1002/ibd.20860] [Citation(s) in RCA: 255] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Escherichia coli, particularly the adherent-invasive E. coli (AIEC) pathovar, has been increasingly implicated in the ethiopathogenesis of Crohn's disease (CD). We describe the richness, abundance, diversity, and pathogenic features of E. coli and AIEC strains that colonize the intestinal mucosa. METHODS Approximately 100 E. coli colonies per biopsy from 20 CD patients (18 biopsies from colon and 23 from ileum) and 28 healthy controls (C) (25, colon; 27, ileum) were isolated. Repetitive extragenic palindrome-polymerase chain reaction (Rep-PCR) and pulsed field gel electrophoresis (PFGE) were used to analyze the clonality of isolates. For AIEC identification, adhesion and invasion assays were performed over Intestine-407 cells, and the capacity to survive and replicate intracellularly was determined over macrophages J774. The serotypes, phylotypes, and genotypes (19 virulence genes) of strains were also investigated. RESULTS Mucosa-associated E. coli richness (E. coli subtypes/patient: C = 2.0 +/- 1.0; CD = 2.1 +/- 1.3) and diversity (Shannon Index: H'(C): 2.1 +/- 0.6; H'(CD): 2.5 +/- 0.8) were similar between CD and C, but higher E. coli counts were characteristic of CD patients (P = 0.010), particularly those with Crohn's ileitis (P = 0.001). Host-specific pulsotypes shared virulence features of ExPEC at similar frequencies between CD and C, except for iucD, which was more prevalent in E. coli from controls (C: 75%, CD: 40%, P = 0.027). In contrast, greater AIEC prevalence (% subjects with AIEC: CD = 51.9%; C = 16.7%; P = 0.003), abundance (% AIEC/E. coli: CD = 3.8 +/- 5.0%; C = 1.5 +/- 3.8%; P = 0.039), and richness (number of AIEC subtypes: CD = 0.8 +/- 1.4; C = 0.2 +/- 0.4; P = 0.015) of E. coli strains belonging to the AIEC pathovar was observed for CD patients. AIEC subtypes showed a high variability of seropathotypes and pulsotypes, although the B2 phylogroup was the most prevalent (AIEC: 64%, non-AIEC: 38%, P = 0.044). CONCLUSIONS New data about ecological parameters of AIEC reinforces the implication of AIEC in CD.
Collapse
|