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Laboratory of pathogenic bacteria


RNDr. Ondřej Černý, Ph.D.


E-mail: ondrej.cerny@natur.cuni.cz, ondrej.cerny@biomed.cas.cz
Phone: +420 296 442 769


Currently at the Institute of Microbiology, Czech Academy of Sciences, v.v.i., from September 2022 we will have our labs also directly at the Department of Genetics and Microbiology, Faculty of Science, Charles University.

Research description:

Establishing a niche suitable for a pathogen inside a new host is a very dynamic process. After the entry into the new host, the pathogen faces several barriers. This results in dramatic decrease in pathogen population size. Three possible scenarios may happen: a) the host successfully eliminate the pathogen (locally), b) the pathogen establishes a niche suitable for its survival and replication or c) the balance is reached when the host controls the infection but fails to clear it completely. Clearly, all three scenarios happen in a limited space and at the same time during one infection event. The main questions of our research are i) what predispose certain pathogen cells to colonise a certain niche, ii) what makes this niche permissive for pathogen replication and iii) how the individual local developments shape the final outcome.

Fig. 1: Host – pathogen interaction during the infection. The pathogen cells are destroyed, taken up for antigen presentation and proliferate in a limited space concomitantly. The pathogen can also disseminate throughout the host, e.g. in host cells migrating to local draining lymph nodes. These events influence the quality and quantity of interactions between involved host cells and the events in one infected area thus necessarily influence the events in other areas as well as overall host response to the infection.

In our research, we concentrate on heterogeneity of bacteria in one infected area and between different infected areas and on the changes in cell – cell interaction introduced by the bacteria. As a model for our research, we are using the facultatively intracellular pathogen Salmonella enterica serovar Typhimurium. S. Typhimurium is a causative agent of gastroenteritis accompanied with diarrhoea and can be also used as a model for typhoid fever. Besides various microbiological methods we commonly utilize also flow cytometry and various modern methods of single cell analysis (transcriptomice, microscopy). We currently cooperate mostly with the Laboratory of Infection Biology and the Laboratory od Post-transcriptional Control of Gene Expression at the Microbiological institute, Czech Academy of Sciences, Prague, Czech Republic, as well as with the Typas Group of Systems Microbiology, EMBL, Heidelberg, Germany..

Publications relevant to the above-described research topic can be found, e.g., at the ORCID profile of the Head of the Laboratory, Ondřej Černý, Ph.D. For information on various topics of M.Sc.  or Ph.D. theses that could be done in the Laboratory, or regarding other types of scientific cooperation, please, contact him as well.

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