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Dr. Roman Špánek
Technical university in Liberec

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0 Parallel Computing
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Journal article
Published: 02 May 2021 in Antibiotics
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Clostridioides difficile is the most common pathogen responsible for hospital-acquired diarrhea. This complication of antibiotic treatment mainly endangers the health of elder patients. Preventing the development of C. difficile infections (CDI) is still a challenge that needs to be addressed. In our study, the results of 872 C. difficile positive stool samples were used to describe the epidemiological situation affected by a change in the prescription of fluoroquinolone antibiotics. In a total, 93 of strains were typed by polymerase chain reaction (PCR) and capillary gel electrophoresis. Between years 2014 and 2018 the decline in the fluoroquinolones consumption was 69.3 defined daily dose (DDD) per 1000 patient-days (from 103.3 to 34.0), in same period CDI incidence declined by 1.3 cases per 10,000 patient-bed days (from 5.6 to 4.3). Results of epidemiologic and statistical analysis shows that decline in fluoroquinolones consumption has significant influence on CDI incidence and prevalence of hypervirulent strains. In the University Hospital Hradec Králové properly managed antibiotic stewardship policy has reduced CDI incidence by 23.2% and lowered rate of hypervirulent ribotypes 001 and 176.

ACS Style

Kristýna Vaverková; Martin Kracík; Lenka Ryšková; Pavla Paterová; Rudolf Kukla; Lenka Hobzová; Roman Špánek; Helena Žemličková. Effect of Restriction of Fluoroquinolone Antibiotics on Clostridioides difficile Infections in the University Hospital Hradec Králové. Antibiotics 2021, 10, 519 .

AMA Style

Kristýna Vaverková, Martin Kracík, Lenka Ryšková, Pavla Paterová, Rudolf Kukla, Lenka Hobzová, Roman Špánek, Helena Žemličková. Effect of Restriction of Fluoroquinolone Antibiotics on Clostridioides difficile Infections in the University Hospital Hradec Králové. Antibiotics. 2021; 10 (5):519.

Chicago/Turabian Style

Kristýna Vaverková; Martin Kracík; Lenka Ryšková; Pavla Paterová; Rudolf Kukla; Lenka Hobzová; Roman Špánek; Helena Žemličková. 2021. "Effect of Restriction of Fluoroquinolone Antibiotics on Clostridioides difficile Infections in the University Hospital Hradec Králové." Antibiotics 10, no. 5: 519.

Article
Published: 01 February 2021 in Current Microbiology
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The application of zero-valent iron particles (ZVI) for the treatment of heavily polluted environment and its biological effects have been studied for at least two decades. Still, information on the impact on bacterial metabolic pathways is lacking. This study describes the effect of microscale and nanoscale ZVI (mZVI and nZVI) on the abundance of different metabolic pathways in freshwater bacterial communities. The metabolic pathways were inferred from metabolism modelling based on 16S rRNA gene sequence data using paprica pipeline. The nZVI changed the abundance of numerous metabolic pathways compared to a less influencing mZVI. We identified the 50 most affected pathways, where 31 were related to degradation, 17 to biosynthesis, and 2 to detoxification. The linkage between pathways was two times higher in nZVI samples compared to mZVI, and was specifically higher considering the arsenate detoxification II pathway. Limnohabitans and Roseiflexus were linked to the same pathways in both nZVI and mZVI. The prediction of metabolic pathways increases our knowledge of the impacts of nZVI and mZVI on freshwater bacterioplankton.

ACS Style

Nhung H. A. Nguyen; Roman Špánek; Priscila Falagan-Lotsch; Alena Ševců. Impact of Zero-Valent Iron on Freshwater Bacterioplankton Metabolism as Predicted from 16S rRNA Gene Sequence Libraries. Current Microbiology 2021, 78, 979 -991.

AMA Style

Nhung H. A. Nguyen, Roman Špánek, Priscila Falagan-Lotsch, Alena Ševců. Impact of Zero-Valent Iron on Freshwater Bacterioplankton Metabolism as Predicted from 16S rRNA Gene Sequence Libraries. Current Microbiology. 2021; 78 (3):979-991.

Chicago/Turabian Style

Nhung H. A. Nguyen; Roman Špánek; Priscila Falagan-Lotsch; Alena Ševců. 2021. "Impact of Zero-Valent Iron on Freshwater Bacterioplankton Metabolism as Predicted from 16S rRNA Gene Sequence Libraries." Current Microbiology 78, no. 3: 979-991.

Journal article
Published: 16 November 2020 in Journal of Hazardous Materials
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Compacted bentonites are one of the best sealing and backfilling clays considered for use in Deep Geological Repositories of radioactive wastes. However, an in-depth understanding of their behavior after placement in the repository is required, including if the activity of indigenous microorganisms affects safety conditions. Here we provide an optimized phenol:chloroform based protocol that facilitates higher DNA-yields when other methods failed. To demonstrate the efficiency of this method, DNA was extracted from acetate-treated bentonites compacted at 1.5 and 1.7 g/cm3 densities after 24 months anoxic incubation. Among the 16S rRNA gene sequences identified, those most similar to taxa mediating biogeochemical sulfur cycling included sulfur oxidizing (e.g., Thiobacillus, and Sulfurimonas) and sulfate reducing (e.g., Desulfuromonas and Desulfosporosinus) bacteria. In addition, iron-cycling populations included iron oxidizing (e.g., Thiobacillus and Rhodobacter) plus reducing taxa (e.g., Geobacillus). Genera described for their capacity to utilize acetate as a carbon source were also detected such as Delftia and Stenotrophomonas. Lastly, microscopic analyses revealed pores and cracks that could host nanobacteria or spores. This study highlights the potential role of microbial driven biogeochemical processes in compacted bentonites and the effect of high compaction on microbial diversity in Deep Geological Repositories.

ACS Style

Cristina Povedano-Priego; Fadwa Jroundi; Margarita Lopez-Fernandez; Rojina Shrestha; Roman Spanek; Inés Martín-Sánchez; María Victoria Villar; Alena Ševců; Mark Dopson; Mohamed L. Merroun. Deciphering indigenous bacteria in compacted bentonite through a novel and efficient DNA extraction method: Insights into biogeochemical processes within the Deep Geological Disposal of nuclear waste concept. Journal of Hazardous Materials 2020, 408, 124600 .

AMA Style

Cristina Povedano-Priego, Fadwa Jroundi, Margarita Lopez-Fernandez, Rojina Shrestha, Roman Spanek, Inés Martín-Sánchez, María Victoria Villar, Alena Ševců, Mark Dopson, Mohamed L. Merroun. Deciphering indigenous bacteria in compacted bentonite through a novel and efficient DNA extraction method: Insights into biogeochemical processes within the Deep Geological Disposal of nuclear waste concept. Journal of Hazardous Materials. 2020; 408 ():124600.

Chicago/Turabian Style

Cristina Povedano-Priego; Fadwa Jroundi; Margarita Lopez-Fernandez; Rojina Shrestha; Roman Spanek; Inés Martín-Sánchez; María Victoria Villar; Alena Ševců; Mark Dopson; Mohamed L. Merroun. 2020. "Deciphering indigenous bacteria in compacted bentonite through a novel and efficient DNA extraction method: Insights into biogeochemical processes within the Deep Geological Disposal of nuclear waste concept." Journal of Hazardous Materials 408, no. : 124600.

Journal article
Published: 01 September 2020 in International Journal of Systematic and Evolutionary Microbiology
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A fructose-6-phosphate phosphoketolase-positive strain (GSD1FST) was isolated from a faecal sample of a 3 weeks old German Shepherd dog. The closest related taxa to isolate GSD1FST based on results from the EZBioCloud database were Bifidobacterium animalis subsp. animalis ATCC 25527T, Bifidobacterium animalis subsp. lactis DSM 10140T and Bifidobacterium anseris LMG 30189T, belonging to the Bifidobacterium pseudolongum phylogenetic group. The resulting 16S rRNA gene identities (compared length of 1454 nucleotides) towards these taxa were 97.30, 97.23 and 97.09 %, respectively. The pairwise similarities of strain GSD1FST using argS, atpA, fusA, hsp60, pyrG, rpsC, thrS and xfp gene fragments to all valid representatives of the B. pseudolongum phylogenetic group were in the concatenated range of 83.08–88.34 %. Phylogenomic analysis based on whole-genome methods such as average nucleotide identity revealed that bifidobacterial strain GSD1FST exhibits close phylogenetic relatedness (88.17 %) to Bifidobacetrium cuniculi LMG 10738T. Genotypic characteristics and phylogenetic analyses based on nine molecular markers, as well as genomic and comparative phenotypic analyses, clearly proved that the evaluated strain should be considered as representing a novel species within the B. pseudolongum phylogenetic group named as Bifidobacterium canis sp. nov. (GSD1FST=DSM 105923T=LMG 30345T=CCM 8806T).

ACS Style

Vera Neuzil-Bunesova; Gabriele Andrea Lugli; Nikol Modrackova; Marie Makovska; Jakub Mrazek; Chahrazed Mekadim; Sarka Musilova; Ivona Svobodova; Roman Spanek; Marco Ventura; Jiri Killer. Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris). International Journal of Systematic and Evolutionary Microbiology 2020, 70, 5040 -5047.

AMA Style

Vera Neuzil-Bunesova, Gabriele Andrea Lugli, Nikol Modrackova, Marie Makovska, Jakub Mrazek, Chahrazed Mekadim, Sarka Musilova, Ivona Svobodova, Roman Spanek, Marco Ventura, Jiri Killer. Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris). International Journal of Systematic and Evolutionary Microbiology. 2020; 70 (9):5040-5047.

Chicago/Turabian Style

Vera Neuzil-Bunesova; Gabriele Andrea Lugli; Nikol Modrackova; Marie Makovska; Jakub Mrazek; Chahrazed Mekadim; Sarka Musilova; Ivona Svobodova; Roman Spanek; Marco Ventura; Jiri Killer. 2020. "Bifidobacterium canis sp. nov., a novel member of the Bifidobacterium pseudolongum phylogenetic group isolated from faeces of a dog (Canis lupus f. familiaris)." International Journal of Systematic and Evolutionary Microbiology 70, no. 9: 5040-5047.

Journal article
Published: 22 January 2020 in Water
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A stall of cis-1,2-DCE and vinyl chloride (VC) is frequently observed during bioremediation of groundwater chloroethenes via reductive dechlorination. These chloroethenes may be oxidised by aerobic methanotrophs or ethenotrophs co-metabolically and/or metabolically. We assessed the potential for such oxidation at 12 sites (49 groundwater samples) using hydrochemical and molecular biological tools. Both ethenotroph (etnC and etnE) and methanotroph (mmoX and pmoA) functional genes were identified in 90% of samples, while reductive dehalogenase functional genes (vcrA and bvcA) were identified in 82%. All functional genes were simultaneously detected in 78% of samples, in actively biostimulated sites in 88% of samples. Correlation analysis revealed that cis-1,2-DCE concentration was positively correlated with vcrA, etnC and etnE, while VC concentration was correlated with etnC, etnE, vcrA and bvcA. However, feature selection based on random forest classification indicated a significant relationship for the vcrA in relation to cis-1,2-DCE, and vcrA, bvcA and etnE for VC and no prove of relationship between cis-1,2-DCE or VC and the methanotroph functional genes. Analysis of hydrochemical parameters indicated that aerobic oxidation of chloroethenes by ethenotrophs may take place under a range of redox conditions of aquifers and coincide with high ethene and VC concentrations.

ACS Style

Jan Němeček; Kristýna Marková; Roman Špánek; Vojtěch Antoš; Petr Kozubek; Ondřej Lhotský; Miroslav Černík. Hydrochemical Conditions for Aerobic/Anaerobic Biodegradation of Chlorinated Ethenes—A Multi-Site Assessment. Water 2020, 12, 322 .

AMA Style

Jan Němeček, Kristýna Marková, Roman Špánek, Vojtěch Antoš, Petr Kozubek, Ondřej Lhotský, Miroslav Černík. Hydrochemical Conditions for Aerobic/Anaerobic Biodegradation of Chlorinated Ethenes—A Multi-Site Assessment. Water. 2020; 12 (2):322.

Chicago/Turabian Style

Jan Němeček; Kristýna Marková; Roman Špánek; Vojtěch Antoš; Petr Kozubek; Ondřej Lhotský; Miroslav Černík. 2020. "Hydrochemical Conditions for Aerobic/Anaerobic Biodegradation of Chlorinated Ethenes—A Multi-Site Assessment." Water 12, no. 2: 322.

Research articles
Published: 06 December 2019 in Corrosion Engineering, Science and Technology
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Carbon steel is currently being considered as a candidate canister material for use in a deep geological repository of radioactive waste. Assessment of canister material corrosion through microbial activity is an important part of the safety assessment for the final repository. The aim of study was to compare and characterise the corrosion behaviour of carbon steel under sterile and non-sterile anaerobic conditions in natural groundwater containing sulphate-reducing bacteria (SRB). A molecular-biological approach was used to determine the presence and abundance changes of relevant bacterial groups. Carbon steel corrosion rates were higher in the presence of SRB compared with sterile control. EIS described the evolution of three time-constants under non-sterile conditions, while scanning electron microscopy confirmed that the carbon steel surface was covered with a two-layer biofilm. Molecular-biological analysis of the water and biofilm indicated the dominance of SRB, with Desulfomicrobium and Desulfovibrio species prevalent.

ACS Style

Tomáš Černoušek; Rojina Shrestha; Hana Kovářová; Roman Špánek; Alena Ševců; Kristína Sihelská; Jakub Kokinda; Jan Stoulil; Jana Steinová. Microbially influenced corrosion of carbon steel in the presence of anaerobic sulphate-reducing bacteria. Corrosion Engineering, Science and Technology 2019, 55, 127 -137.

AMA Style

Tomáš Černoušek, Rojina Shrestha, Hana Kovářová, Roman Špánek, Alena Ševců, Kristína Sihelská, Jakub Kokinda, Jan Stoulil, Jana Steinová. Microbially influenced corrosion of carbon steel in the presence of anaerobic sulphate-reducing bacteria. Corrosion Engineering, Science and Technology. 2019; 55 (2):127-137.

Chicago/Turabian Style

Tomáš Černoušek; Rojina Shrestha; Hana Kovářová; Roman Špánek; Alena Ševců; Kristína Sihelská; Jakub Kokinda; Jan Stoulil; Jana Steinová. 2019. "Microbially influenced corrosion of carbon steel in the presence of anaerobic sulphate-reducing bacteria." Corrosion Engineering, Science and Technology 55, no. 2: 127-137.

Journal article
Published: 25 July 2019 in Chemosphere
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ISCO using activated sodium persulphate is a widely used technology for treating chlorinated solvent source zones. In sensitive areas, however, high groundwater sulphate concentrations following treatment may be a drawback. In situ biogeochemical transformation, a technology that degrades contaminants via reduced iron minerals formed by microbial activity, offers a potential solution for such sites, the bioreduction of sulphate and production of iron sulphides that abiotically degrade chlorinated ethenes acting as a ‘polishing technology’ following ISCO. This study assesses this approach in the field using hydrochemical and molecular tools, solid phase analysis and geochemical modelling. Following a neutralisation and bioaugmentation, favourable conditions for iron- and sulphate-reducers were created, resulting in a remarkable increase in their relative abundance. The abundance of dechlorinating bacteria (Dehalococcoides mccartyi, Dehalobacter sp. and Desulfitobacterium spp.) remained low throughout this process. The activity of iron- and sulphate-reducers was further stimulated through application of magnetite plus starch and microiron plus starch, resulting in an increase in ferrous iron concentration (from

ACS Style

Jan Němeček; Magda Nechanická; Roman Špánek; František Eichler; Josef Zeman; Miroslav Černík. Engineered in situ biogeochemical transformation as a secondary treatment following ISCO – A field test. Chemosphere 2019, 237, 124460 .

AMA Style

Jan Němeček, Magda Nechanická, Roman Špánek, František Eichler, Josef Zeman, Miroslav Černík. Engineered in situ biogeochemical transformation as a secondary treatment following ISCO – A field test. Chemosphere. 2019; 237 ():124460.

Chicago/Turabian Style

Jan Němeček; Magda Nechanická; Roman Špánek; František Eichler; Josef Zeman; Miroslav Černík. 2019. "Engineered in situ biogeochemical transformation as a secondary treatment following ISCO – A field test." Chemosphere 237, no. : 124460.

Journal article
Published: 10 July 2018 in The ISME Journal
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Combining a minimum food web model with Arctic microbial community dynamics, we have suggested that top-down control by copepods can affect the food web down to bacterial consumption of organic carbon. Pursuing this hypothesis further, we used the minimum model to design and analyse a mesocosm experiment, studying the effect of high (+Z) and low (-Z) copepod density on resource allocation, along an organic-C addition gradient. In the Arctic, both effects are plausible due to changes in advection patterns (affecting copepods) and meltwater inputs (affecting carbon). The model predicts a trophic cascade from copepods via ciliates to flagellates, which was confirmed experimentally. Auto- and heterotrophic flagellates affect bacterial growth rate and abundance via competition for mineral nutrients and predation, respectively. In +Z, the model predicts low bacterial abundance and activity, and little response to glucose; as opposed to clear glucose consumption effects in –Z. We observed a more resilient bacterial response to high copepods and demonstrate this was due to changes in bacterial community equitability. Species able to use glucose to improve their competitive and/or defensive properties, became predominant. The observed shift from a SAR11-to a Psychromonodaceae – dominated community suggests the latter was pivotal in this modification of ecosystem function. We argue that this group used glucose to improve its defensive or its competitive abilities (or both). Adding such flexibility in bacterial traits to the model, we show how it creates the observed resilience to top-down manipulations observed in our experiment.

ACS Style

Tatiana M. Tsagaraki; Bernadette Pree; Øystein Leiknes; Aud Larsen; Gunnar Bratbak; Lise Øvreås; Jorun K. Egge; Roman Spanek; Maria Lund Paulsen; Yngvar Olsen; Olav Vadstein; T. F. Thingstad. Bacterial community composition responds to changes in copepod abundance and alters ecosystem function in an Arctic mesocosm study. The ISME Journal 2018, 12, 2694 -2705.

AMA Style

Tatiana M. Tsagaraki, Bernadette Pree, Øystein Leiknes, Aud Larsen, Gunnar Bratbak, Lise Øvreås, Jorun K. Egge, Roman Spanek, Maria Lund Paulsen, Yngvar Olsen, Olav Vadstein, T. F. Thingstad. Bacterial community composition responds to changes in copepod abundance and alters ecosystem function in an Arctic mesocosm study. The ISME Journal. 2018; 12 (11):2694-2705.

Chicago/Turabian Style

Tatiana M. Tsagaraki; Bernadette Pree; Øystein Leiknes; Aud Larsen; Gunnar Bratbak; Lise Øvreås; Jorun K. Egge; Roman Spanek; Maria Lund Paulsen; Yngvar Olsen; Olav Vadstein; T. F. Thingstad. 2018. "Bacterial community composition responds to changes in copepod abundance and alters ecosystem function in an Arctic mesocosm study." The ISME Journal 12, no. 11: 2694-2705.