Antibiotic resistance, molecular epidemiology, mass spectrometry
128
Scopus Publications
Scopus Publications
Clonal outbreak of an extensively drug-resistant NDM-1 producing Pseudomonas aeruginosa in a local hospital in the Czech Republic Katerina Chudejova, Tsolaire Sourenian, Marc Finianos, Anna Sramkova, Costas C. Papagiannitsis, Jaroslav Hrabak, Ibrahim Bitar Microbiology Spectrum, 2026 A clonal outbreak of 18 ST773 NDM-1 producing Pseudomonas aeruginosa strains has been detected for the first time in the Czech Republic. The strains were extremely drug-resistant (XDR) and resistant to serum killing. SNP-based phylogeny and CRISPR assay typing showed minimal genomic variations among the isolates. The results suggest a high-risk, persistent, virulent clone causing the hospital outbreak, with the possibility of a nationwide outbreak. IMPORTANCE Our research on the novel detection of the NDM-1 gene in carbapenem-resistant Pseudomonas aeruginosa ST773 in the Czech Republic is of great significance for public health and infection control. Until now, the emergence of this gene in P. aeruginosa strains was uncommon in this region, as carbapenem resistance was primarily associated with IMP and VIM types of MBLs. This nosocomial outbreak was triggered by an index case patient repatriated from areas with reported NDM-1 producing P. aeruginosa , illustrating how international travel contributes to the spread of such resistant pathogens. The results obtained in this study show that it is necessary to focus on tracing the source of infections to control and prevent nosocomial infections, helping to protect public health in the Czech Republic.
Emergence of carbapenemase-producing Escherichia coli in acute care hospitals in 32 European countries (the CCRE survey): a prospective, multicentre, cross-sectional, epidemiological, microbiological, and genomic surveillance study Sophia David, Anke Kohlenberg, Corin Yeats, Khalil Abu-Dahab, Barbara Albiger, Nabil-Fareed Alikhan, Erik Alm, Sara Byfors, Natacha Couto, Julio Diaz Caballero, Christian G Giske, Corinna Glasner, Marius Linkevicius, Erika Matuschek, Daniel Palm, Olov Svartström, Hajo Grundmann, Marc J Struelens, Karin Tegmark Wisell, Dominique L Monnet, Inga Fröding, David M Aanensen, Alma Brolund, Andi Koraqi, Artan Bego, Petra Apfalter, Rainer Hartl, Te-Din Huang, Katrien Latour, Maja Travar, Stefana Sabtcheva, Arjana Tambić-Andrašević, Jaroslav Hrabák, Helena Žemličková, Panayiota Maikanti Charalambous, Anette M Hammerum, Anastasia Bilozor, Marika Jürna-Ellam, Jari Jalava, Kati Räisänen, Laurent Dortet, Ines Noll, Niels Pfennigwerth, Kyriaki Tryfinopoulou, Alkiviadis Vatopoulos, Ákos Tóth, Kristjan Orri Helgason, Martin Cormican, Maria Del Grosso, Maria Giufrè, Arsim Kurti, Lul Raka, Baiba Niedre-Otomere, Jelena Razmuk, Jekaterina Sinotova, Marie Meo, Monique Perrin, Denise Micallef, Nina Nestorova, Milena Lopičić, Vineta Vuksanović, Antoni P A Hendrickx, Karuna E W Vendrik, Ana Kaftandzieva, Dugagjin Osmani, Ørjan Samuelsen, Elżbieta Literacka, Manuela Caniça, Vera Manageiro, Irina Codita, Brandusa Lixandru, Ivana Ćirković, Deana Medić, Milan Nikš, Mateja Pirš, Belén Aracil, Jesús Oteo Iglesias, Petra Edquist, Karin Westmo, Hüsniye Şimşek, Serap Süzük Yildiz, Katie L Hopkins, Danièle Meunier Lancet Microbe, 2026 Background The emergence of carbapenem resistance in Escherichia coli is of major concern due to the high propensity of spread of this species and scarce treatment options. Herein, we examined the occurrence and spread of carbapenem-resistant E coli based on the carbapenem-resistant and/or colistin-resistant Enterobacterales (CCRE) survey performed across European countries in 2019. Methods We analysed epidemiological, microbiological, and whole-genome sequencing data of 548 E coli isolates from individual patients from 156 hospitals in 32 European countries over 6 months in 2019. These hospitals collected the first ten successive isolates of carbapenem-resistant or carbapenem-susceptible increased exposure (carbapenem-R/I) Klebsiella pneumoniae species complex or E coli, and carbapenem-susceptible (carbapenem-S) comparator isolates of the same species. Antimicrobial susceptibility testing was performed for 19 antimicrobial agents. Whole-genome sequencing was performed centrally using Illumina technology. Isolates from the CCRE survey were compared with those from the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) study. Findings Of the 548 E coli isolates, 211 (38·5%) were carbapenem-resistant or susceptible, increased exposure (carbapenem-R/I), and 337 (61·5%) were carbapenem-susceptible (carbapenem-S). Five sequence types (STs) accounted for 96 (45·5%) of 211 carbapenem-R/I isolates: ST131 (27), ST410 (20), ST38 (19), ST167 (16), and ST648 (14). Carbapenemase genes were identified in 182 (86·3%) carbapenem-R/I isolates, a pronounced increase from the 2013–14 EuSCAPE study (36 of 99, 36·4%). The most common genes were bla NDM−5 (62 of 182, 34·1%) and bla OXA−48 (40 of 182, 22·0%). bla NDM−5 carriage increased substantially compared with that in EuSCAPE (two of 99, 2·02%). Phylogenetic analysis showed substantial clonal spread of globally disseminated bla NDM−5 -harbouring lineages, with numerous introductions into Europe but minimal onward transmission. Interpretation High-risk STs of E coli carrying carbapenemase genes are rapidly spreading globally, although our results indicate that, in 2019, most cases in Europe were sporadic. We urge vigilant monitoring, including genomic surveillance, and strengthening of control efforts, to reduce mortality and morbidity associated with the impending rise in carbapenem-R/I E coli cases. Funding European Centre for Disease Prevention and Control and the Centre for Genomic Pathogen Surveillance.
Persistent spread of carbapenemase-producing Klebsiella pneumoniae in acute care hospitals in 36 European countries (the CCRE survey): a prospective, multicentre, cross-sectional, epidemiological, microbiological, and genomic surveillance study Inga Fröding, Sophia David, Corin Yeats, Khalil Abu-Dahab, Barbara Albiger, Nabil-Fareed Alikhan, Erik Alm, Sara Byfors, Natacha Couto, Julio Diaz Caballero, Christian G Giske, Erika Matuschek, Marius Linkevicius, Daniel Palm, Olov Svartström, Marc J Struelens, Karin Tegmark Wisell, Dominique L Monnet, Alma Brolund, David M Aanensen, Anke Kohlenberg, Andi Koraqi, Artan Bego, Petra Apfalter, Rainer Hartl, Te-Din Huang, Katrien Latour, Maja Travar, Stefana Sabtcheva, Arjana Tambić-Andrašević, Jaroslav Hrabák, Helena Žemličková, Panayiota Maikanti Charalambous, Anette M Hammerum, Anastasia Bilozor, Marika Jürna-Ellam, Jari Jalava, Kati Räisänen, Laurent Dortet, Ines Noll, Niels Pfennigwerth, Kyriaki Tryfinopoulou, Alkiviadis Vatopoulos, Ákos Tóth, Kristjan Orri Helgason, Martin Cormican, Giulia Errico, Monica Monaco, Arsim Kurti, Lul Raka, Baiba Niedre-Otomere, Jelena Razmuk, Jekaterina Sinotova, Marie Meo, Monique Perrin, Denise Micallef, Nina Nestorova, Milena Lopičić, Vineta Vuksanović, Daan Notermans, Karuna E W Vendrik, Ana Kaftandzieva, Dugagjin Osmani, Ørjan Samuelsen, Elżbieta Literacka, Manuela Caniça, Vera Manageiro, Irina Codita, Brandusa Lixandru, Ivana Ćirković, Deana Medić, Milan Nikš, Mateja Pirš, Javier E Cañada-García, María Pérez-Vázquez, Petra Edquist, Karin Westmo, Hüsniye Şimşek, Serap Süzük Yildiz, Katie L Hopkins, Danièle Meunier Lancet Microbe, 2026 BACKGROUND: Carbapenem-resistant Enterobacterales pose a substantial threat to patients and health-care systems. We conducted a survey of carbapenem-resistant and/or colistin-resistant Enterobacterales (CCRE survey) in 37 European countries to describe their occurrence, geographical distribution, and population dynamics and inform control policies. We report the results of Klebsiella pneumoniae species complex isolates in this study. METHODS: In this cross-sectional, epidemiological, microbiological, and genomic study conducted in all EU, European Economic Area and EU candidate countries as of 2019, hospital microbiology laboratories were selected on the basis of population coverage. Participating laboratories collected, from patient samples, the first ten successive isolates of carbapenem-resistant or carbapenem-susceptible increased exposure (carbapenem-R/I) K pneumoniae species complex or Escherichia coli, and carbapenem-susceptible (carbapenem-S) comparator isolates of the same species, accompanied by patient epidemiological and clinical information. Isolate collection started in 2019, with three possible starting dates-ie, March 1, April 1, or May 1, 2019, and ended after collection of ten carbapenem-R/I and carbapenem-S isolates or a maximum period of 6 months. Isolates were tested for phenotypic susceptibility to 16 antimicrobial agents of relevance to K pneumoniae species complex. Whole-genome sequencing was performed centrally using Illumina technology. Isolates from the CCRE survey were compared with those from the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) study. FINDINGS: 1566 carbapenem-R/I and 1407 carbapenem-S K pneumoniae species complex isolates collected from patients in 302 hospitals in 36 countries (one country did not send isolates) were analysed in this study. The high-risk lineages identified during a previous similar survey in 2013-14 (EuSCAPE) were found to continue to circulate across European hospitals in 2019 (ST11, ST15, ST101, and ST258/512). Moreover, concerning shifts in the pathogen population were observed. First, a higher proportion of carbapenem-R/I isolates was found to carry a carbapenemase gene in the CCRE survey (1398 [89·3%] of 1566) than in EuSCAPE (657 [69·6%] of 944), mainly related to increased acquisition of carbapenemase genes by high-risk lineages. Of note, among ST307 isolates from all hospitals, the proportion of carbapenem-R/I isolates carrying a carbapenemase gene increased from 14 (60·9%) of 23 in EuSCAPE to 164 (91·1%) of 180 in the CCRE survey. Second, an expansion of emerging multidrug-resistant lineages (ST147, ST307, and ST39) was also noted: Among 113 hospitals that contributed K pneumoniae species complex isolates to both EuSCAPE and the CCRE survey, the proportion of ST147 increased from 16 (3·4%) of 476 in EuSCAPE to 49 (7·4%) of 662 carbapenem-R/I isolates in the CCRE survey, that of ST307 increased from 15 (3·2%) of 476 to 88 (13·3%) of 662, and that of ST39 increased from 3 (0·6%) of 476 to 10 (1·5%) of 662. Third, there was an increased spread of isolates harbouring acquired virulence loci: isolates with the highest Kleborate virulence score of five increased from 7 (0·4%) of 1717 in EuSCAPE to 40 (1·3%) of 2973 in the CCRE survey. Notably, the increase was mainly observed in the carbapenem-S-group. INTERPRETATION: The survey findings portray an escalating epidemiological situation and suggest that control measures have not been able to interrupt transmission of high-risk lineages of carbapenemase-producing K pneumoniae in European hospitals. The heterogeneous and evolving situation with regards to circulating lineages and dominant carbapenemase genes requires strengthening and continuous adaptation of diagnostic, treatment, and control measures guided by genomic surveillance. FUNDING: European Centre for Disease Prevention and Control and Centre for Genomic Pathogen Surveillance.
Proof-of-concept MALDI-TOF-MS assay for the detection of Toxin B enzymatic activity in Clostridioides difficile infection Josef Dvorak, Lukáš Fojtík, Ljubina Adámková, Katerina Vlkova, Vendula Studentova, Katerina Chudejova, Lenka Geigerová, Michael Volny, Petr Novak, Jaroslav Hrabak, Petr Pompach Microbiology Spectrum, 2025 Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometers have become an integral part of all modern clinical microbiology laboratories. They serve as the key tool for pathogen identification and antibiotic resistance determination. However, certain limiting conditions must be fulfilled. The pathogen cannot be tested directly from the sample and requires the cultivation of a pure colony, which means that the standard protocol takes additional time, workforce, and consumables. The testing protocol is also more complicated when it comes to anaerobes. In our work, we focused on the functional detection of Clostridioides difficile , an important nosocomial human pathogen that is responsible for diarrhea and can lead to life-threatening colitis, as a model diagnostic problem. The virulence of C. difficile is mainly caused by two toxins, Toxin A and Toxin B. Established diagnostic methods, including nucleic acid amplification testing methods and immunoassays, detect the presence of the microorganism or the presence and concentration of the toxins, with limited ability to gauge infection severity based on the actual biochemical activity of the toxins and thus their potency to cause harm. This work presents proof-of-concept assays that indirectly determine the toxin activity in the human stool, a very complex matrix sample, using the natural RhoA protein as substrate. The RhoA protein substrate was recombinantly prepared with biotin tag modification, which allows its attachment to the NeutrAvidin MALDI chips. In the assay, the RhoA substrate anchored on the MALDI chip undergoes enzymatic glycosylation when exposed to the Toxin B in the stool sample, and the reaction product is then detected by MALDI-TOF mass spectrometry directly from the MALDI chip. The entire assay, from sampling to final mass spectrometry detection, was performed in situ , on the NeutrAvidin MALDI chip, which was prepared by unique surface modification technology also described in this work. The assay was successfully tested for the detection of Toxin B in a cohort of patient samples as well as in cell culture of C. difficile . IMPORTANCE The diagnostics of Clostridioides difficile infection is usually based on the identification of the bacterial pathogen and/or on the detection of the Toxins A and B. Due to the variance in Toxins A and B activity across species, the toxin concentration determined by standard methods does not necessarily correlate with the severity of the disease. Assays that would target toxins’ enzymatic activity are not routinely used because the requirements are unsuitable for clinical laboratories. In this study, we demonstrate a new approach that determines the presence and potency of Toxin B indirectly by determining its enzymatic activity rather than its concentration. This is performed by detecting mass difference due to glycosylation of RhoA substrate by Toxin B, which is then determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The presented proof-of-concept assay thus offers the possibility to quickly determine the activity of C. difficile toxins directly in the stool samples without pathogen cultivation.
Mass spectrometric profiling of microbial polysaccharides using laser desorption/ionization – time-of-flight (LDI-TOF) and liquid chromatography-mass spectrometry (LC-MS): a novel method for structural fingerprinting and derivatization Lucia Dadovska, Veronika Paskova, Petr Novak, Jaroslav Hrabak Frontiers in Cellular and Infection Microbiology, 2025 IntroductionOver the last two decades, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced into the routine diagnostic practice of microbiological laboratories for the rapid taxonomic identification of bacteria and yeasts. However, a method that effectively identifies microbes directly from clinical samples using MALDI-TOF MS has not yet been found. One of the promising targets is microbial polysaccharides, which are abundant structures in bacterial and fungal cells. Their rapid and inexpensive analysis, nevertheless, is complicated. This study focused on detecting microbial polysaccharides, such as lipopolysaccharides, using MALDI-TOF MS and liquid chromatography-tandem mass spectrometry (LC-MS). We developed a method for fingerprinting polysaccharides by acid hydrolysis and enzymatic digestion.MethodsThe mono- and oligosaccharides are then derivatized with a newly designed probe (vanillyl pararosaniline, the HD ligand), enabling efficient ionization without the use of the MALDI matrix. For precise analysis of polysaccharides, the hydroxyl groups can be esterified by formic acid.ResultsThe method was validated using several saccharides as well as Escherichia coli lipopolysaccharides (O26:B6, O55:B5, and O111:B4). Derivatization using the HD ligand also allows the detection of structures containing amines and phosphate groups in positive ion mode. We optimized the method using crude bacteria (Escherichia coli, Salmonella enterica, Shigella dysenteriae, Shigella boydii, Shigella flexneri, and Legionella pneumophila, Staphylococcus aureus) and yeasts (Candida albicans, C. kudriavzevii, and C. tropicalis).DiscussionThis approach opens the possibility of directly detecting microbial polysaccharides from clinical specimens. Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (LDI-TOF MS) using a specific self-ionizable ligand enables direct ionization without the need for an additional matrix, allowing for the particular detection of molecules of interest while suppressing the background signal.
A novel F type plasmid encoding mcr-10 in a clinical Enterobacter ludwigii strain from a tertiary hospital in the Czech Republic Tsolaire Sourenian, Jana Palkovicova, Costas C. Papagiannitsis, Monika Dolejska, Jaroslav Hrabak, Ibrahim Bitar Journal of Global Antimicrobial Resistance, 2024 OBJECTIVE: Here we describe a novel IncFIA plasmid harbouring mcr-10 gene in a clinical Enterobacter ludwigii strain isolated at the University Hospital in Pilsen in the Czech Republic. METHODS: The strain was subjected to antibiotic susceptibility testing. Whole genome sequencing was performed using Illumina for short-read sequencing and Oxford Nanopore Technologies for long-read sequencing followed by hybrid assembly. The resulting genome was used to detect species using average nucleotide identity, resistance genes, plasmid replicon and MLST (using centre for genomic epidemiology databases; ResFinder, PlasmidFinder and MLST, respectively) and virulence genes using VFDB. RESULTS: Τhe strain showed susceptibility against tetracycline, cefuroxime and chloramphenicol, and it was susceptible to the second and third generation of cephalosporins, carbapenems and colistin. Genome analysis identified the strain as E. ludwigii sequence type ST20 and located the mcr-10 gene on an IncFIA (HI1)/IncFII (Yp) plasmid (pI9455333_MCR10; 129 863 bp). Upon blasting the nucleotide sequence of pI9455333_MCR10 against the NCBI database, no similar plasmid sequence was detected, implying a novel plasmid structure. Nevertheless, it showed a partial similarity with pRHBSTW-00123_3 and FDAARGOS 1432, which were detected in Enterobacter cloacae complex (ECC) strains in wastewater samples in 2017 in UK and in 2021 in the United States, respectively, and pEC81-mcr, which was detected in a clinical Escherichia coli strain in 2020 in China. Moreover, I9455333cz genome carried virulence genes coding for curli fibers, fimbrial adherence determinants, siderophore aerobactin, iron uptake proteins and regulators of sigma factor. CONCLUSION: In conclusion, we identified a novel IncF plasmid harbouring mcr-10 gene in a clinical Enterobacter ludwigii strain. To our knowledge, this is the first clinical report of mcr-10 in the Czech Republic.
Spread of carbapenemase-producing Morganella spp from 2013 to 2021: a comparative genomic study Rémy A Bonnin, Elodie Creton, Amandine Perrin, Delphine Girlich, Cecile Emeraud, Agnès B Jousset, Mathilde Duque, Aymeric Jacquemin, Katie Hopkins, Pierre Bogaerts, Youri Glupczynski, Niels Pfennigwerth, Marek Gniadkowski, Antoni P A Hendrickx, Kim van der Zwaluw, Petra Apfalter, Rainer Hartl, Vendula Studentova, Jaroslav Hrabak, Gerald Larrouy-Maumus, Eduardo P C Rocha, Thierry Naas, Laurent Dortet Lancet Microbe, 2024 BACKGROUND: Morganella spp are opportunistic pathogens involved in various infections. Intrinsic resistance to multiple antibiotics (including colistin) combined with the emergence of carbapenemase producers reduces the number of active antimicrobials. The aim of this study was to characterise genetic features related to the spread of carbapenem-resistant Morganella spp. METHODS: This comparative genomic study included extensively drug-resistant Morganella spp isolates collected between Jan 1, 2013, and March 1, 2021, by the French National Reference Center (NRC; n=68) and European antimicrobial resistance reference centres in seven European countries (n=104), as well as one isolate from Canada, two reference strains from the Pasteur Institute collection (Paris, France), and two colistin-susceptible isolates from Bicêtre Hospital (Kremlin-Bicêtre, France). The isolates were characterised by whole-genome sequencing, antimicrobial susceptibility testing, and biochemical tests. Complete genomes from GenBank (n=103) were also included for genomic analysis, including phylogeny and determination of core genomes and resistomes. Genetic distance between different species or subspecies was performed using average nucleotide identity (ANI). Intrinsic resistance mechanisms to polymyxins were investigated by combining genetic analysis with mass spectrometry on lipid A. FINDINGS: Distance analysis by ANI of 275 isolates identified three groups: Morganella psychrotolerans, Morganella morganii subspecies sibonii, and M morganii subspecies morganii, and a core genome maximum likelihood phylogenetic tree showed that the M morganii isolates can be separated into four subpopulations. On the basis of these findings and of phenotypic divergences between isolates, we propose a modified taxonomy for the Morganella genus including four species, Morganella psychrotolerans, Morganella sibonii, Morganella morganii, and a new species represented by a unique environmental isolate. We propose that M morganii include two subspecies: M morganii subspecies morganii (the most prevalent) and M morganii subspecies intermedius. This modified taxonomy was supported by a difference in intrinsic resistance to tetracycline and conservation of metabolic pathways such as trehalose assimilation, both only present in M sibonii. Carbapenemase producers were mostly identified among five high-risk clones of M morganii subspecies morganii. The most prevalent carbapenemase corresponded to NDM-1, followed by KPC-2, and OXA-48. A cefepime-zidebactam combination was the most potent antimicrobial against the 172 extensively drug-resistant Morganella spp isolates in our collection from different European countries, which includes metallo-β-lactamase producers. Lipid A analysis showed that the intrinsic resistance to colistin was associated with the presence of L-ARA4N on lipid A. INTERPRETATION: This global characterisation of, to our knowledge, the widest collection of extensively drug-resistant Morganella spp highlights the need to clarify the taxonomy and decipher intrinsic resistance mechanisms, and paves the way for further genomic comparisons. FUNDING: None.
Genomic characterization of ST38 NDM-5-producing Escherichia coli isolates from an outbreak in the Czech Republic Katerina Chudejova, Tsolaire Sourenian, Jana Palkovicova, Katarina Stredanska, Lucie Nechutna, Katerina Vlkova, Vendula Studentova, Jaroslav Hrabak, Costas C. Papagiannitsis, Monika Dolejska, Ibrahim Bitar, Marian Glasnak, Dana Krckova, Beata Horvathova, Jana Jurankova, Renata Tejkalova, Zora Pokorna, Vladimir Fibiger, David Sus, Marian Mednansky, Lenka Ryskova, Miriam Koupilova, Jana Kotalikova, Miroslava Prejzkova, Marie Bohackova, Marie Smolikova, Helena Skacan, Denisa Vesela, Blanka Puchalkova, Galina Eliasova, Helena Nedvedova, Lenka Unuckova, Yvona Barinkova, Hana Kremeckova, Daniela Fackova, Jana Janeckova, Roman Jirsa, Roman Zaruba, Eva Vesela, Dana Zamazalova, Marie Dovalova, Iva Vagnerova, Vladimir Kurfurst, Blanka Ochvatova, Eva Chmelarova, Eva Krejci, Eva Zalabska, Vera Kurkova, Simona Blahova, Tamara Bergerova, Vaclava Adamkova, Jan Kubele, Marketa Skruzna, Daniela Balikova, Alena Steinerova, Zuzana Semerakova, Miloslava Kocianova, Martina Curdova, Helena Zemlickova, Vladislav Jakubu, Zuzana Kadleckova, Elka Nycova, Helena Jordakova, Otakar Nyc, Filip Prusik, Ivana Kohnova, Renata Holnova, Eva Simeckova, Erika Czyzova, Alice Kucharova, Ladislav Trojan, Danuta Urbusova, Eva Vitova, Jana Repiscakova, Jarmila Miklova, Lenka Dvorakova, Jirina Jiresova, Jan Tkadlec, Zdena Pitakova, Natasa Bartonikova, Michal Stanek, and Antimicrobial Agents and Chemotherapy, 2024 A 2-year national genomic screening in the Czech Republic identified a notable prevalence of the New Delhi metallo-β-lactamase 5 (NDM-5)-producing Escherichia coli sequence type 38 (ST38) in the city of Brno. Forty-two ST38 E. coli isolates harbored the bla NDM-5 gene on the chromosome. Virulence factors confirmed the persistence of these isolates through biofilm formation. Single Nucleotide Polymorphisms (SNPs)-based phylogeny and CRISPR assay typing showed minimal genomic variations, implying a clonally driven outbreak. Results suggest that this high-risk clone may impose a nationwide problem.
Simultaneous PCR detection of Paenibacillus larvae targeting insertion sequence IS256 and Melissococcus plutonius targeting pMP1 plasmid from hive specimens Katerina Vlkova, Tomas Erban, Martin Kamler, Dalibor Titera, Ibrahim Bitar, Jaroslav Hrabak Folia Microbiologica, 2024 Paenibacillus larvae and Melissococcus plutonius represent the most threatening bacterial diseases of honeybee (Apis mellifera)—American and European foulbrood, respectively. For efficient control of those diseases, rapid and accurate detection of the pathogens is crucial. Therefore, we developed a novel multiplex PCR method simultaneously detecting both pathogens. To design and optimize multiplex PCR reaction, four strains of P. larvae representing four ERIC genotypes I–IV (strain DSM 7030—ERIC I, DSM 25430—ERIC II, LMG 16252—ERIC III, DSM 3615—ERIC IV) were selected. Those strains were fully sequenced using long-read sequencing (Sequel I, Pacific Biosciences). For P. larvae, the multicopy insertion sequence IS256 identified in all genotypes of P. larvae was selected to provide high sensitivity. M. plutonius was detected by plasmid pMP1 sequence and the virulence verified by following detection of ETX/MTX2 toxin responsible for pore formation in the cell membrane. As an internal control, a gene encoding for major royal jelly protein 1 specific for honeybees was selected. The method was validated on 36 clinical specimens collected from the colonies suffering from American and European foulbrood in the Czech Republic. Based on the results, sensitivity of PCR was calculated to 93.75% and specificity to 100% for P. larvae diagnosed from hive debris and 100% sensitivity and specificity for honeybee workers and larval scales as well as for diseased brood infected by M. plutonius.
Quality of MALDI-TOF mass spectra in routine diagnostics: results from an international external quality assessment including 36 laboratories from 12 countries using 47 challenging bacterial strains Aline Cuénod, Martina Aerni, Claudia Bagutti, Banu Bayraktar, Efe Serkan Boz, Cynthia Beisert Carneiro, Carlo Casanova, Alix T. Coste, Peter Damborg, Dirk W. van Dam, Mehmet Demirci, Pavel Drevinek, Olivier Dubuis, José Fernandez, Gilbert Greub, Jaroslav Hrabak, Gülen Hürkal Yiğitler, Jakub Hurych, Thøger Gorm Jensen, Géraldine Jost, Greetje A. Kampinga, Sonja Kittl, Christine Lammens, Claudia Lang, Reto Lienhard, Julie Logan, Carola Maffioli, Ivana Mareković, Matthias Marschal, Jacob Moran-Gilad, Oliver Nolte, Michael Oberle, Michael Pedersen, Valentin Pflüger, Sigrid Pranghofer, Julia Reichl, Rob J. Rentenaar, Arnaud Riat, Belén Rodríguez-Sánchez, Camille Schilt, Ann-Kathrin Schlotterbeck, Jacques Schrenzel, Shani Troib, Elise Willems, Mandy Wootton, Dominik Ziegler, Adrian Egli Clinical Microbiology and Infection, 2023
Gut microbiome diversity of porcine peritonitis model of sepsis Miroslava Chalupova, Jan Horak, Lenka Kramna, Lukas Nalos, Milan Stengl, Katerina Chudejova, Lucie Kraftova, Ondrej Cinek, Pavel Klein, Martin Matejovic, Jaroslav Hrabak Scientific Reports, 2022
Multicentre study on the reproducibility of MALDI-TOF MS for nontuberculous mycobacteria identification David Rodriguez-Temporal, Fernando Alcaide, Ivana Mareković, James Anthony O’Connor, Rebecca Gorton, Jakko van Ingen, An Van den Bossche, Genevieve Héry-Arnaud, Clémence Beauruelle, Dorothea Orth-Höller, Juan-José Palacios-Gutiérrez, Griselda Tudó, Germán Bou, Pieter-Jan Ceyssens, Montserrat Garrigó, Julià González-Martin, Gilbert Greub, Jaroslav Hrabak, André Ingebretsen, Maria Concepción Mediavilla-Gradolph, Marina Oviaño, Begoña Palop, Arthur B. Pranada, Lidia Quiroga, Maria Jesús Ruiz-Serrano, Belén Rodríguez-Sánchez Scientific Reports, 2022
Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread Sophia David, , Sandra Reuter, Simon R. Harris, Corinna Glasner, Theresa Feltwell, Silvia Argimon, Khalil Abudahab, Richard Goater, Tommaso Giani, Giulia Errico, Marianne Aspbury, Sara Sjunnebo, Edward J. Feil, Gian Maria Rossolini, David M. Aanensen, Hajo Grundmann, and Nature Microbiology, 2019
Igra methods in the routine operation-quantiferon®-tb gold or t-spot.tb? Epidemiologie Mikrobiologie Imunologie, 2016
Detection of β-lactamases and their activity using MALDI-TOF MS Jaroslav Hrabak, Vladimír Havlicek, Costas C. Papagiannitsis Applications of Mass Spectrometry in Microbiology from Strain Characterization to Rapid Screening for Antibiotic Resistance, 2016
Prevalence study on carbapenemase-producing Escherichia coli and Klebsiella pneumoniae isolates in Czech hospitals – results from Czech part of European survey on carbapenemase- -Producing Enterobacteriaceae (EuSCAPE) Epidemiologie Mikrobiologie Imunologie, 2015
Interpretation of the susceptibility test results in enterobacteria producing 3rd- and 4th-generation cephalosporin- or carbapenem-hydrolyzing β-lactamases Epidemiologie Mikrobiologie Imunologie, 2011
The use of molecular genetics techniques in clinical microbiology - Final report from the workshop of the molecular microbiology working group TIDE Epidemiologie Mikrobiologie Imunologie, 2010
Lymphogranuloma venereum: In the Czech Republic already? Cesko Slovenska Dermatologie, 2010
Mobile genetic elements in the epidemiology of bacterial resistance to antibiotics Epidemiologie Mikrobiologie Imunologie, 2010
First identification of metallo-beta-lactamase-producing Pseudomonas aeruginosa in the Czech Republic. Euro Surveillance Bulletin Europeen Sur Les Maladies Transmissibles European Communicable Disease Bulletin, 2009
Carbapenem resistance in enterobacteria Epidemiologie Mikrobiologie Imunologie, 2008
