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Bonet-Rossinyol Q, Camprubí-Font C, López-Siles M, Martinez-Medina M. Identification of differences in gene expression implicated in the Adherent-Invasive Escherichia coli phenotype during in vitro infection of intestinal epithelial cells. Front Cell Infect Microbiol 2023; 13:1228159. [PMID: 37767199 PMCID: PMC10519790 DOI: 10.3389/fcimb.2023.1228159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/21/2023] [Indexed: 09/29/2023] Open
Abstract
Introduction Adherent-invasive Escherichia coli (AIEC) is strongly associated with the pathogenesis of Crohn's disease (CD). However, no molecular markers currently exist for AIEC identification. This study aimed to identify differentially expressed genes (DEGs) between AIEC and non-AIEC strains that may contribute to AIEC pathogenicity and to evaluate their utility as molecular markers. Methods Comparative transcriptomics was performed on two closely related AIEC/non-AIEC strain pairs during Intestine-407 cell infection. DEGs were quantified by RT-qPCR in the same RNA extracts, as well as in 14 AIEC and 23 non-AIEC strains to validate the results across a diverse strain collection. Binary logistical regression was performed to identify DEGs whose quantification could be used as AIEC biomarkers. Results Comparative transcriptomics revealed 67 differences in expression between the two phenotypes in the strain pairs, 50 of which (81.97%) were corroborated by RT-qPCR. When explored in the whole strain collection, 29 DEGs were differentially expressed between AIEC and non-AIEC phenotypes (p-value < 0.042), and 42 genes between the supernatant fraction of infected cell cultures and the cellular fraction containing adhered and intracellular bacteria (p-value < 0.049). Notably, six DEGs detected in the strain collection were implicated in arginine biosynthesis and five in colanic acid synthesis. Furthermore, two biomarkers based on wzb and cueR gene expression were proposed with an accuracy of ≥ 85% in our strain collection. Discussion This is the first transcriptomic study conducted using AIEC-infected cell cultures. We have identified several genes that may be involved in AIEC pathogenicity, two of which are putative biomarkers for identification.
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Mayorgas A, Dotti I, Martínez-Picola M, Esteller M, Bonet-Rossinyol Q, Ricart E, Salas A, Martínez-Medina M. A Novel Strategy to Study the Invasive Capability of Adherent-Invasive Escherichia coli by Using Human Primary Organoid-Derived Epithelial Monolayers. Front Immunol 2021; 12:646906. [PMID: 33854511 PMCID: PMC8039293 DOI: 10.3389/fimmu.2021.646906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [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: 01/08/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Over the last decades, Adherent-Invasive Escherichia coli (AIEC) has been linked to the pathogenesis of Crohn’s Disease. AIEC’s characteristics, as well as its interaction with the gut immune system and its role in intestinal epithelial barrier dysfunction, have been extensively studied. Nevertheless, the currently available techniques to investigate the cross-talk between this pathogen and intestinal epithelial cells (IECs) are based on the infection of immortalized cell lines. Despite their many advantages, cell lines cannot reproduce the conditions in tissues, nor do they reflect interindividual variability or gut location-specific traits. In that sense, the use of human primary cultures, either healthy or diseased, offers a system that can overcome all of these limitations. Here, we developed a new infection model by using freshly isolated human IECs. For the first time, we generated and infected monolayer cultures derived from human colonic organoids to study the mechanisms and effects of AIEC adherence and invasion on primary human epithelial cells. To establish the optimal conditions for AIEC invasion studies in human primary organoid-derived epithelial monolayers, we designed an infection-kinetics study to assess the infection dynamics at different time points, as well as with two multiplicities of infection (MOI). Overall, this method provides a model for the study of host response to AIEC infections, as well as for the understanding of the molecular mechanisms involved in adhesion, invasion and intracellular replication. Therefore, it represents a promising tool for elucidating the cross-talk between AIEC and the intestinal epithelium in healthy and diseased tissues.
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Affiliation(s)
- Aida Mayorgas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Isabella Dotti
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Marta Martínez-Picola
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Miriam Esteller
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Queralt Bonet-Rossinyol
- Laboratory of Molecular Microbiology, Department of Biology, Universitat de Girona, Girona, Spain
| | - Elena Ricart
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
| | - Azucena Salas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBER-EHD, Barcelona, Spain
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Portell-Buj E, Bonet-Rossinyol Q, López-Gavín A, Roman A, Fernández-Pittol M, Tudó G, Gonzalez-Martin J. Comparison of two-drug combinations, amikacin/tigecycline/imipenem and amikacin/tigecycline/clarithromycin against Mycobacteroides abscessus subsp. abscessus using the in vitro time-kill assay. J Antibiot (Tokyo) 2021; 74:285-290. [PMID: 33420382 PMCID: PMC8005373 DOI: 10.1038/s41429-020-00392-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/26/2020] [Accepted: 11/09/2020] [Indexed: 12/03/2022]
Abstract
Nontuberculous mycobacteria include 198 mycobacterial species. Among these, Mycobacteroides abscessus is a rapidly growing mycobacteria that causes lung and skin infections. M. abscessus lung infections are difficult to treat due to the high levels of resistance to several classes of antibiotics. The current treatment is based on combining at least two or three antibiotics. However, treatment outcomes remain very poor. The objective was to compare the in vitro activity of amikacin, tigecycline, imipenem, and clarithromycin, alone and in two different three-drug combinations (amikacin/tigecycline/imipenem and amikacin/tigecycline/clarithromycin) against seven M. abscessus subsp. abscessus clinical isolates using the time-kill assay. The two combinations showed greater activity than the antibiotics tested individually. Even though both combinations showed similar activity as well as no antagonistic activity, the combination including imipenem could not be an alternative treatment against M. abscessus subsp. abscessus lung infections caused by clarithromycin susceptible isolates. However, this combination could be considered against clarithromycin resistant isolates. Future studies are necessary to confirm this hypothesis.
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Affiliation(s)
- Elena Portell-Buj
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Servei de Microbiologia, CDB, Hospital Clínic de Barcelona-ISGlobal, c/ Villarroel 170, 08036, Barcelona, Spain
| | - Queralt Bonet-Rossinyol
- Servei de Microbiologia, CDB, Hospital Clínic de Barcelona-ISGlobal, Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, c/ Villarroel 170, 08036, Barcelona, Spain.,Laboratory of Molecular Microbiology, Biology Department, University of Girona, Girona, Spain
| | - Alexandre López-Gavín
- Servei de Microbiologia, CDB, Hospital Clínic de Barcelona-ISGlobal, Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, c/ Villarroel 170, 08036, Barcelona, Spain
| | - Angely Roman
- Servei de Microbiologia, CDB, Hospital Clínic de Barcelona-ISGlobal, Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, c/ Villarroel 170, 08036, Barcelona, Spain
| | - Mariana Fernández-Pittol
- Servei de Microbiologia, CDB, Hospital Clínic de Barcelona-ISGlobal, Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, c/ Villarroel 170, 08036, Barcelona, Spain
| | - Griselda Tudó
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Servei de Microbiologia, CDB, Hospital Clínic de Barcelona-ISGlobal, c/ Villarroel 170, 08036, Barcelona, Spain
| | - Julian Gonzalez-Martin
- Servei de Microbiologia, CDB, Hospital Clínic de Barcelona-ISGlobal, Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, c/ Villarroel 170, 08036, Barcelona, Spain.
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