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Identification of commensal Escherichia coli genes involved in biofilm resistance to pathogen colonization.

Da Re S, Valle J, Charbonnel N, Beloin C, Latour-Lambert P, Faure P, Turlin E, Le Bouguénec C, Renauld-Mongénie G, Forestier C, Ghigo JM - PLoS ONE (2013)

Bottom Line: We showed that pathogens trigger specific responses in commensal bacteria and we identified genes involved in limiting colonization of incoming pathogens within commensal biofilm.We demonstrated that the absence of yiaF and bssS (yceP) differentially alters pathogen colonization in the mouse gut.This study therefore identifies previously uncharacterized colonization resistance genes and provides new approaches to unravelling molecular aspects of commensal/pathogen competitive interactions.

View Article: PubMed Central - PubMed

Affiliation: Institut Pasteur, Unité de Génétique des Biofilms, Département de Microbiologie, Paris, France.

ABSTRACT
Protection provided by host bacterial microbiota against microbial pathogens is a well known but ill-understood property referred to as the barrier effect, or colonization resistance. Despite recent genome-wide analyses of host microbiota and increasing therapeutic interest, molecular analysis of colonization resistance is hampered by the complexity of direct in vivo experiments. Here we developed an in vitro-to-in vivo approach to identification of genes involved in resistance of commensal bacteria to exogenous pathogens. We analyzed genetic responses induced in commensal Escherichia coli upon entry of a diarrheagenic enteroaggregative E. coli or an unrelated Klebsiella pneumoniae pathogen into a biofilm community. We showed that pathogens trigger specific responses in commensal bacteria and we identified genes involved in limiting colonization of incoming pathogens within commensal biofilm. We tested the in vivo relevance of our findings by comparing the extent of intestinal colonization by enteroaggregative E. coli and K. pneumoniae pathogens in mice pre-colonized with E. coli wild type commensal strain, or mutants corresponding to identified colonization resistance genes. We demonstrated that the absence of yiaF and bssS (yceP) differentially alters pathogen colonization in the mouse gut. This study therefore identifies previously uncharacterized colonization resistance genes and provides new approaches to unravelling molecular aspects of commensal/pathogen competitive interactions.

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Colonization resistance genes are strain-specific.Comparison of the effect on colonization of mutations introduced into commensal MG1655 F′ (C) or into pathogenic strain 55989a (P). Results are represented as ratio of colonization of mutant mixed MG1655 F′Δgene (C*) +P or C+55989aΔgene (P*) biofilms compared to wild-type mixed C+P biofilm. Black bar represents extent of wild-type colonization in C+P mixed biofilms arbitrarily set to one. White bars represent colonization levels of CΔgene +P mixed biofilm (mutation introduced into commensal and wild-type pathogens). Light gray bars represent colonization levels of C+PΔgene mixed biofilm formed by wild-type commensal and mutant pathogens. Names of deleted genes are indicated under the line. Results are averages of at least 6 replicates ± standard deviation of the mean. Asterisks indicate mutant mixed biofilm with a colonization level significantly different from that of wild-type MG1655 F′ + 55989a mixed C+P biofilm, P<0.05.
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pone-0061628-g003: Colonization resistance genes are strain-specific.Comparison of the effect on colonization of mutations introduced into commensal MG1655 F′ (C) or into pathogenic strain 55989a (P). Results are represented as ratio of colonization of mutant mixed MG1655 F′Δgene (C*) +P or C+55989aΔgene (P*) biofilms compared to wild-type mixed C+P biofilm. Black bar represents extent of wild-type colonization in C+P mixed biofilms arbitrarily set to one. White bars represent colonization levels of CΔgene +P mixed biofilm (mutation introduced into commensal and wild-type pathogens). Light gray bars represent colonization levels of C+PΔgene mixed biofilm formed by wild-type commensal and mutant pathogens. Names of deleted genes are indicated under the line. Results are averages of at least 6 replicates ± standard deviation of the mean. Asterisks indicate mutant mixed biofilm with a colonization level significantly different from that of wild-type MG1655 F′ + 55989a mixed C+P biofilm, P<0.05.

Mentions: Finally, we tested whether yiaF, stfE, rcsA, yliE and ypjC could also play a reciprocal role in E. coli 55989a ability to colonize a commensal biofilm. While stfE was absent from the 55989 genome, a ypjC mutant could not be obtained despite repeated attempts. We therefore introduced only a yiaF, rcsA or yliE mutation in the 55989a strain, and we showed that none of these 3 mutations had a significant effect on colonization outcome, suggesting that the observed colonization phenotypes specifically affected pathogen colonization in commensal biofilm, but not the reverse (Fig. 3). Taken together, these results indicated that colonization of commensal MG1655 F′ biofilm by the diarrheagenic pathogenic strain 55989a triggers expression of commensal genes contributing to colonization resistance to the pathogen.


Identification of commensal Escherichia coli genes involved in biofilm resistance to pathogen colonization.

Da Re S, Valle J, Charbonnel N, Beloin C, Latour-Lambert P, Faure P, Turlin E, Le Bouguénec C, Renauld-Mongénie G, Forestier C, Ghigo JM - PLoS ONE (2013)

Colonization resistance genes are strain-specific.Comparison of the effect on colonization of mutations introduced into commensal MG1655 F′ (C) or into pathogenic strain 55989a (P). Results are represented as ratio of colonization of mutant mixed MG1655 F′Δgene (C*) +P or C+55989aΔgene (P*) biofilms compared to wild-type mixed C+P biofilm. Black bar represents extent of wild-type colonization in C+P mixed biofilms arbitrarily set to one. White bars represent colonization levels of CΔgene +P mixed biofilm (mutation introduced into commensal and wild-type pathogens). Light gray bars represent colonization levels of C+PΔgene mixed biofilm formed by wild-type commensal and mutant pathogens. Names of deleted genes are indicated under the line. Results are averages of at least 6 replicates ± standard deviation of the mean. Asterisks indicate mutant mixed biofilm with a colonization level significantly different from that of wild-type MG1655 F′ + 55989a mixed C+P biofilm, P<0.05.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646849&req=5

pone-0061628-g003: Colonization resistance genes are strain-specific.Comparison of the effect on colonization of mutations introduced into commensal MG1655 F′ (C) or into pathogenic strain 55989a (P). Results are represented as ratio of colonization of mutant mixed MG1655 F′Δgene (C*) +P or C+55989aΔgene (P*) biofilms compared to wild-type mixed C+P biofilm. Black bar represents extent of wild-type colonization in C+P mixed biofilms arbitrarily set to one. White bars represent colonization levels of CΔgene +P mixed biofilm (mutation introduced into commensal and wild-type pathogens). Light gray bars represent colonization levels of C+PΔgene mixed biofilm formed by wild-type commensal and mutant pathogens. Names of deleted genes are indicated under the line. Results are averages of at least 6 replicates ± standard deviation of the mean. Asterisks indicate mutant mixed biofilm with a colonization level significantly different from that of wild-type MG1655 F′ + 55989a mixed C+P biofilm, P<0.05.
Mentions: Finally, we tested whether yiaF, stfE, rcsA, yliE and ypjC could also play a reciprocal role in E. coli 55989a ability to colonize a commensal biofilm. While stfE was absent from the 55989 genome, a ypjC mutant could not be obtained despite repeated attempts. We therefore introduced only a yiaF, rcsA or yliE mutation in the 55989a strain, and we showed that none of these 3 mutations had a significant effect on colonization outcome, suggesting that the observed colonization phenotypes specifically affected pathogen colonization in commensal biofilm, but not the reverse (Fig. 3). Taken together, these results indicated that colonization of commensal MG1655 F′ biofilm by the diarrheagenic pathogenic strain 55989a triggers expression of commensal genes contributing to colonization resistance to the pathogen.

Bottom Line: We showed that pathogens trigger specific responses in commensal bacteria and we identified genes involved in limiting colonization of incoming pathogens within commensal biofilm.We demonstrated that the absence of yiaF and bssS (yceP) differentially alters pathogen colonization in the mouse gut.This study therefore identifies previously uncharacterized colonization resistance genes and provides new approaches to unravelling molecular aspects of commensal/pathogen competitive interactions.

View Article: PubMed Central - PubMed

Affiliation: Institut Pasteur, Unité de Génétique des Biofilms, Département de Microbiologie, Paris, France.

ABSTRACT
Protection provided by host bacterial microbiota against microbial pathogens is a well known but ill-understood property referred to as the barrier effect, or colonization resistance. Despite recent genome-wide analyses of host microbiota and increasing therapeutic interest, molecular analysis of colonization resistance is hampered by the complexity of direct in vivo experiments. Here we developed an in vitro-to-in vivo approach to identification of genes involved in resistance of commensal bacteria to exogenous pathogens. We analyzed genetic responses induced in commensal Escherichia coli upon entry of a diarrheagenic enteroaggregative E. coli or an unrelated Klebsiella pneumoniae pathogen into a biofilm community. We showed that pathogens trigger specific responses in commensal bacteria and we identified genes involved in limiting colonization of incoming pathogens within commensal biofilm. We tested the in vivo relevance of our findings by comparing the extent of intestinal colonization by enteroaggregative E. coli and K. pneumoniae pathogens in mice pre-colonized with E. coli wild type commensal strain, or mutants corresponding to identified colonization resistance genes. We demonstrated that the absence of yiaF and bssS (yceP) differentially alters pathogen colonization in the mouse gut. This study therefore identifies previously uncharacterized colonization resistance genes and provides new approaches to unravelling molecular aspects of commensal/pathogen competitive interactions.

Show MeSH
Related in: MedlinePlus