Molecular Microbiology - Alois Čížek
Molecular Microbiology - Alois Čížek


Prof. Alois Čížek Prof. Alois Čížek
Research group leader

Research areas

  • Veterinary Bacteriology (Alois Čížek)
  • Antimicrobial Resistance (Monika Dolejská)
  • Molecular Virology (Vladimír Celer)
  • Epidemiology of tick-borne diseases (Ivan Literák, Pavel Široký)

Main objectives

  • To isolate, identify and characterize abundant anaerobic bacteria colonising intestinal tract of poultry and pigs
  • To investigate the anaerobes and LAB (lactic acid bacteria) for their potential probiotic properties
  • To study the genetic background and molecular epidemiology of avian pathogenic Escherichia coli (APEC) and bacterial fish pathogens (Aeromonas salmonicida, Flavobacterium psychrophilum)
  • To evaluate the occurrence of Enterobacteriaceae and enterococci resistant to clrinically important antimicrobials in human and non-human sources
  • To understand the structure, plasticity and evolution of epidemic plasmids and their potential to spread antibiotic resistance and persist in bacterial communities
  • To study the feature of multi-drug resistant bacterial clones and reasons behind their worldwide emergence
  • To develop the  recombinant virus proteins for diagnostic use and vaccine production
  • To find out fundamental niches of most important tick vectors
  • To define evolutionary relationships and population structure within specific tick-pathogen systems

Content of research

We perform research in the field of veterinary microbiology, with different research aspects:

Veterinary Bacteriology. Newly constituted research subgroup performs research focused on understanding the functions and interactions of bacteria colonising intestinal tract of poultry and pigs. MALDI-TOF MS (matrix assisted laser desorption ionization-time of flight mass spectrometry) and culturomics approach is applied in order to characterize abundant anaerobic bacteria including previously uncultured intestinal bacteria.  Laboratory collection of isolates is pre-selected by MALDI Biotyper using in-house database and identified by sequencing of 16S rRNA. Subsequently in vitro evaluation of potential probiotic properties of pure cultures and co-feeding studies with mixed cultures are performed.  Host response to the inoculation of candidate probiotic cultures is assessed on one-day chick model in collaboration with Veterinary Research Institute Brno (Ivan Rychlik Lab).

The application of molecular biology techniques in veterinary bacteriology is almost endless and clears the way for insight into the genetic background of bacterial pathogens and their properties (e. g. clonality, virulence associated factors, antimicrobial resistance). With this intention, we characterize especially APEC,  Aeromonas salmonicida and Flavobacterium psychrophilum isolates in close collaboration with Antibiotic Resistance Subgroup (Monika Dolejská).

Antimicrobial Resistance. The worldwide dissemination of emerging resistance mechanisms via successful mobile genetic elements such as plasmids is a growing concern in current epidemiology and both human and veterinary medicine. Our research is focused on plasmids and their role in transmission of antibiotic resistance genes. We aim to understand how resistance genes are mobilized and spread in bacterial populations since it is a desirable pre-requisite to combat rapidly increasing antibiotic resistance. Plasmid-encoded genes impact bacterial physiology and lifestyle with consequent dramatic effect on the adaptation and evolution of host bacteria. Some groups of plasmids associated with resistance to critically important antibiotics are currently considered as “epidemic resistance plasmids”, being isolated from various bacterial species of Enterobacteriaceae family and wide range of sources, including humans, animals and the environment. Apart from antibiotic resistance genes these epidemic plasmids can carry genetic information for virulence, genes for catabolic pathways and resistance to toxic compounds. It has been proposed that plasmids can be maintained even in the absence of antibiotic selective pressure and they can also increase the overall fitness of their bacterial host. Our research is therefore focused on various aspects of epidemic plasmids using comparative genomics, complete plasmid sequencing and annotation, plasmid transfer and fitness cost experiments. We also study interactions and co-evolution between the plasmid and various host bacteria, aiming to reveal the reasons behind the success of epidemic resistance plasmids.


Molecular Virology. The virology research subgroup complement research activities of CEITEC VFU Brno by targeting animal virus infection, development of diagnostic tests and development of virus vaccines. The subgroup can thus contribute to projects dealing with animal complex infections and vaccines.

Tick/vector-borne diseases. The biology of vectors and vector-borne diseases is another field of the RG. Since the distribution and spreading of numerous species of vectors acquired a new dynamic during last two decades, the discovery and exact defining of ecological and climatic variables influencing these current changeovers will help us formulate the most imperilled areas in respect to specific vector borne diseases. We concentrate on the study of the distribution, spread, and risk levels of selected tick/vector-borne diseases. 

Overview of the research approach and methodology (Antimicrobial Resistance Subgroup)


All news