BackgroundOn 29 January 2024, the European Centre for Disease Prevention and Control distributed an alert about a metronidazole-resistant Clostridioides difficile outbreak of PCR ribotype (RT) 955 in England.AimWe aimed to investigate the presence of RT955 in Czech, Slovak and Polish C. difficile isolates and evaluate different culture media for detecting its metronidazole resistance.MethodsIsolates with binary toxin genes identified as 'unknown' by the WEBRIBO PCR ribotyping database up to 2023 were re-analysed after adding the RT955 profile to the database. The RT955 isolates were characterised by whole genome sequencing and tested for susceptibility to 15 antimicrobials.ResultsWe did not find RT955 in Czech (n = 6,661, 2012-2023) and Slovak (n = 776, 2015-2023) isolates, but identified 13 RT955 cases (n = 303, 2021-2023) in three hospitals in Poland. By whole genome multilocus sequence typing, 10 isolates clustered into one clonal complex including a sequence of United Kingdom strain ERR12670107, and shared similar antimicrobial resistance genes/mutations. All 13 isolates were resistant to ciprofloxacin/moxifloxacin, erythromycin/clindamycin and ceftazidime. All isolates had a mutation in the nimB gene promoter and in NimB (Tyr130Ser and Leu155Ile). The metronidazole resistance was detected in all isolates using brain-heart-infusion agar supplemented with haemin and Chocolate agar. Results were discrepant with the European Committee on Antimicrobial Susceptibility Testing-recommended Fastidious anaerobe agar and Brucella blood agar.ConclusionThe identification of clonally related haem-dependent metronidazole-resistant C. difficile RT955 in multiple hospitals indicates a need for prospective surveillance to estimate its prevalence in Europe.

• MeSH
• antibakteriální látky * farmakologie   MeSH
• bakteriální léková rezistence * genetika   MeSH
• Clostridioides difficile * genetika   účinky léků   izolace a purifikace   klasifikace   MeSH
• epidemický výskyt choroby MeSH
• klostridiové infekce * epidemiologie   mikrobiologie   farmakoterapie   MeSH
• lidé MeSH
• metronidazol * farmakologie   MeSH
• mikrobiální testy citlivosti MeSH
• multilokusová sekvenční typizace MeSH
• polymerázová řetězová reakce MeSH
• ribotypizace * MeSH
• sekvenování celého genomu MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH
• Polsko MeSH
• Slovenská republika MeSH

Cíl: Cílem studie byla analýza vlivu pandemie covidu-19 na epidemiologickou situaci invazivního meningokokového onemocnění (IMO) a na molekulární charakteristiky izolátů Neisseria meningitidis způsobujících IMO v České republice. Materiál a metody: Studie vycházela z dat surveillance IMO za období 2018–2024 (k 27. 5. 2024) a analyzovány celogenomovou sekvenací (WGS) byly všechny dostupné izoláty N. meningitidis z IMO z těchto let. Pro analýzu vlivu pandemie covidu-19 bylo sledované období rozděleno na tři srovnávané etapy: pre-covidové období (2018–2019), období pandemie covidu-19 (2020–2022) a post-covidové období (2023–2024). Výsledky: V důsledku zavedení epidemiologických opatření proti pandemii covidu-19 došlo v České republice, podobně jako v ostatních zemích, k poklesu počtu infekčních onemocnění přenášených vzdušnou cestou, včetně IMO. Po uvolnění těchto epidemiologických opatření však nedošlo v České republice k opětnému vzestupu počtu IMO, na rozdíl od řady jiných zemí. Charakterizace izolátů z IMO metodou WGS prokázala, že v průběhu covidového a post-covidového období došlo k postupné změně populace meningokoků, které v České republice působí IMO. U izolátů N. meningitidis séroskupin C, W a Y lze sledovat postupný a výrazný pokles celkové heterogenity – z deseti různých klonálních komplexů zachycených v pre-covidovém období na pouhé tři v post-covidových letech (cc11, cc23 a cc103). Zároveň byla zjištěna významná redukce izolátů N. meningitidis C; cc11. U izolátů N. meningitidis B lze naopak pozorovat nárůst celkové heterogenity během období pandemie covidu-19 a její opětovnou redukci na celkově nejnižší hodnoty v post-covidovém období. Závěr: V přetrvávajícím poklesu počtu IMO v České republice má roli i zavedení úhrady očkování MenB vakcínou a konjugovanou vakcínou A, C, W, Y pro malé děti (v květnu 2020) a pro adolescenty (v lednu 2022). K udržení nízkých počtů IMO v České republice je žádoucí pokračovat v očkování MenB vakcínou a konjugovanou vakcínou A, C, W, Y dle doporučení České vakcinologické společnosti ČLS JEP.

Objective: To analyse the impact of the COVID-19 pandemic on the epidemiological situation of invasive meningococcal disease (IMD) and molecular characteristics of Neisseria meningitidis isolates causing IMD in the Czech Republic. Material and Methods: The study was based on IMD surveillance data for 2018–2024 (as of 27 May 2024), and all available N. meningitidis isolates from IMD of these years were subjected to whole genome sequencing (WGS). To analyse the impact of the COVID-19 pandemic, the study period was divided into three parts: the pre-COVID period (2018–2019), the COVID-19 pandemic period (2020–2022), and the post-COVID period (2023–2024). Results: As a result of the implementation of the COVID-19 control measures, similar to other countries, there has been a decline in the incidence of air-borne infections including IMD in the Czech Republic. However, unlike many other countries, there has not been a resurgence of IMD in the Czech Republic following the release of these epidemiological measures. WGS characterisation of IMD isolates showed a gradual change in the population of meningococci causing IMD in the Czech Republic during the COVID-19 and post-COVID periods. For N. meningitidis isolates of serogroups C, W, and Y, a gradual and significant decline in overall heterogeneity can be observed – from ten different clonal complexes detected in the pre-COVID period to only three in the post-COVID years (cc11, cc23, and cc103). At the same time, a significant reduction was observed in N. meningitidis C isolates; cc11. In contrast, an increase in overall heterogeneity can be observed for N. meningitidis B isolates during the COVID-19 pandemic period, followed by its decline again to overall lowest values in the post-COVID period. Conclusion: The fact that MenB vaccine and conjugate vaccine A, C, W, Y started to be covered by health insurance for young children (in May 2020) and adolescents (in January 2022) also appears to play a role in the persistent decline of IMD in the Czech Republic. In order to maintain the low incidence of IMD in the Czech Republic, it is desirable to continue vaccination with MenB vaccine and conjugated vaccine A, C, W, Y in accordance with the recommendations of the Czech Society of Vaccinology of the Czech Medical Association of Jan Evangelista Purkyně.

• MeSH
• COVID-19 epidemiologie   MeSH
• lidé MeSH
• meningokokové infekce epidemiologie   MeSH
• Neisseria meningitidis * genetika   MeSH
• pandemie MeSH
• sekvenční analýza * MeSH
• vakcinace statistika a číselné údaje   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH

The opportunistic pathogen Candida parapsilosis is a major causative agent of candidiasis leading to death in immunocompromised individuals. Azoles are the first line of defense in their treatment. The purpose of this study was to characterize eight fluconazole-resistant and sensitive C. parapsilosis hospital isolates through a battery of phenotypic tests that target pathogenicity attributes such as virulence, biofilm formation, stress resistance, and ergosterol content. Whole genome sequencing was carried out to identify mutations in key pathogenicity and resistance genes. Phylogenetic comparison was performed to determine strain relatedness and clonality. Genomic data and phylogenetic analysis revealed that two isolates were C. orthopsilosis and C. metapsilosis misidentified as C. parapsilosis. Whole genome sequencing analysis revealed known and novel mutations in key drug resistance and pathogenicity genes such as ALS6, ALS7, SAPP3, SAP7, SAP9, CDR1, ERG6, ERG11 and UPC2. Phylogenetic analysis revealed a high degree of relatedness and clonality within our C. parapsilosis isolates. Our results showed that resistant isolates exhibited an increase in biofilm content compared to the sensitive isolates. In conclusion, our study is the first of its kind in Lebanon to describe phenotypic and genotypic characteristics of nosocomial C. parapsilosis complex isolates having a remarkable ability to form biofilms.

• MeSH
• antifungální látky * farmakologie   MeSH
• biofilmy * růst a vývoj   MeSH
• Candida parapsilosis * genetika   izolace a purifikace   klasifikace   MeSH
• fenotyp * MeSH
• flukonazol farmakologie   MeSH
• fungální léková rezistence * genetika   MeSH
• fylogeneze * MeSH
• genotyp * MeSH
• infekce spojené se zdravotní péčí mikrobiologie   MeSH
• kandidóza * mikrobiologie   MeSH
• lidé MeSH
• mikrobiální testy citlivosti * MeSH
• nemocnice MeSH
• sekvenování celého genomu * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Libanon MeSH

To trace evolution of Panton-Valentine leucocidin-positive clonal complex 398 methicillin-resistant Staphylococcus aureus (MRSA) in the Czech Republic, we tested 103 MRSA isolates from humans. Five (4.9%) were Panton-Valentine leucocidin-positive clonal complex 398, sequence types 1232 and 9181. Spread to the Czech Republic may result from travel to or from other countries.

• MeSH
• bakteriální toxiny * biosyntéza   genetika   MeSH
• dějiny 21. století MeSH
• dospělí MeSH
• exotoxiny * genetika   biosyntéza   MeSH
• leukocidiny * genetika   MeSH
• lidé MeSH
• methicilin rezistentní Staphylococcus aureus * genetika   izolace a purifikace   MeSH
• stafylokokové infekce * mikrobiologie   epidemiologie   MeSH
• Check Tag
• dějiny 21. století MeSH
• dospělí MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• historické články MeSH
• Geografické názvy
• Česká republika MeSH

• MeSH
• cytogenetika MeSH
• terminologie jako téma MeSH

• Konspekt
• Obecná genetika. Obecná cytogenetika. Evoluce
• NLK Obory
• cytologie, klinická cytologie
• genetika, lékařská genetika
• NLK Publikační typ
• kolektivní monografie

Recent studies highlighted genetic aberrations associated with prognosis in Mantle Cell lymphoma (MCL), yet comprehensive testing is not implemented in clinical routine. We conducted a comprehensive genomic characterization of 180 patients from the European MCL network trials by targeted sequencing of peripheral blood DNA using the EuroClonality(EC)-NDC assay. The IGH::CCND1 fusion was identified in 94% of patients, clonal IGH-V-(D)-J rearrangements in all, and 79% had ≥1 somatic gene mutation. The top mutated genes were ATM, TP53, KMT2D, SAMHD1, BIRC3 and NFKBIE. Copy number variations (CNVs) were detected in 83% of patients with RB1, ATM, CDKN2A/B and TP53 being the most frequently deleted and KLF2, CXCR4, CCND1, MAP2K1 and MYC the top amplified genes. CNVs and mutations were more frequently observed in older patients with adverse impact on prognosis. TP53mut, NOTCH1mut, FAT1mut TRAF2del, CDKN2A/Bdel and MAP2K1amp were linked to inferior failure-free (FFS) and overall survival (OS), while TRAF2mut, EGR2del and BCL2amp related to inferior OS only. Genetic complexity (≥3 CNVs) observed in 51% of analysed patients was significantly associated with impaired FFS and OS. We demonstrate that targeted sequencing from peripheral blood and bone marrow reliably detects diagnostically and prognostically important genetic factors in MCL patients, facilitating genetic characterization in clinical routine.

• MeSH
• dospělí MeSH
• genetické testování metody   MeSH
• lidé středního věku MeSH
• lidé MeSH
• lymfom z plášťových buněk * genetika   mortalita   MeSH
• mutace * MeSH
• nádorové biomarkery genetika   MeSH
• prognóza MeSH
• rizikové faktory MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• variabilita počtu kopií segmentů DNA * MeSH
• vysoce účinné nukleotidové sekvenování metody   MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

INTRODUCTION: Reproductive isolation and hybrid sterility are mechanisms that maintain the genetic integrity of species and prevent the introgression of heterospecific genes. However, crosses of closely related species can lead to complex evolution, such as the formation of all-female lineages that reproduce clonally. Bighead catfish (Clarias macrocephalus) and North African catfish (C. gariepinus) diverged 40 million years ago. They are cultivated and hybridized in Thailand for human consumption. Male hybrids are sterile due to genome-wide chromosome asynapsis during meiosis. Although female hybrids are sometimes fertile, their chromosome configuration during meiosis has not yet been studied. METHODS: We analyzed meiosis in the hybrid female catfish at pachytene (synaptonemal complexes) and diplotene (lampbrush chromosomes), using immunostaining to detect chromosome pairing and double-stranded break formation, and FISH with species-specific satellite DNAs to distinguish the parental chromosomes. RESULTS: More than 95% of oocytes exhibited chromosome asynapsis in female hybrid catfish; however, they were able to progress to the diplotene stage and form mature eggs. The remaining oocytes underwent premeiotic endoreplication, followed by synapsis and crossing over between sister chromosomes, similar to known clonal lineages in fish and reptiles. DISCUSSION: The occurrence of clonal reproduction in female hybrid catfish suggests a unique model for studying gametogenic alterations caused by hybridization and their potential for asexual reproduction. Our results further support the view that clonal reproduction in certain hybrid animals relies on intrinsic mechanisms of sexually reproducing parental species, given their multiple independent origins with the same mechanism.

• Publikační typ
• časopisecké články MeSH

UNLABELLED: Lyme disease, caused by spirochetes in the Borrelia burgdorferi sensu lato clade within the Borrelia genus, is transmitted by Ixodes ticks and is currently the most prevalent and rapidly expanding tick-borne disease in Europe and North America. We report complete genome sequences of 47 isolates that encompass all established species in this clade while highlighting the diversity of the widespread human pathogenic species B. burgdorferi. A similar set of plasmids has been maintained throughout Borrelia divergence, indicating that they are a key adaptive feature of this genus. Phylogenetic reconstruction of all sequenced Borrelia genomes revealed the original divergence of Eurasian and North American lineages and subsequent dispersals that introduced B. garinii, B. bavariensis, B. lusitaniae, B. valaisiana, and B. afzelii from East Asia to Europe and B. burgdorferi and B. finlandensis from North America to Europe. Molecular phylogenies of the universally present core replicons (chromosome and cp26 and lp54 plasmids) are highly consistent, revealing a strong clonal structure. Nonetheless, numerous inconsistencies between the genome and gene phylogenies indicate species dispersal, genetic exchanges, and rapid sequence evolution at plasmid-borne loci, including key host-interacting lipoprotein genes. While localized recombination occurs uniformly on the main chromosome at a rate comparable to mutation, lipoprotein-encoding loci are recombination hotspots on the plasmids, suggesting adaptive maintenance of recombinant alleles at loci directly interacting with the host. We conclude that within- and between-species recombination facilitates adaptive sequence evolution of host-interacting lipoprotein loci and contributes to human virulence despite a genome-wide clonal structure of its natural populations. IMPORTANCE: Lyme disease (also called Lyme borreliosis in Europe), a condition caused by spirochete bacteria of the genus Borrelia, transmitted by hard-bodied Ixodes ticks, is currently the most prevalent and rapidly expanding tick-borne disease in the United States and Europe. Borrelia interspecies and intraspecies genome comparisons of Lyme disease-related bacteria are essential to reconstruct their evolutionary origins, track epidemiological spread, identify molecular mechanisms of human pathogenicity, and design molecular and ecological approaches to disease prevention, diagnosis, and treatment. These Lyme disease-associated bacteria harbor complex genomes that encode many genes that do not have homologs in other organisms and are distributed across multiple linear and circular plasmids. The functional significance of most of the plasmid-borne genes and the multipartite genome organization itself remains unknown. Here we sequenced, assembled, and analyzed whole genomes of 47 Borrelia isolates from around the world, including multiple isolates of the human pathogenic species. Our analysis elucidates the evolutionary origins, historical migration, and sources of genomic variability of these clinically important pathogens. We have developed web-based software tools (BorreliaBase.org) to facilitate dissemination and continued comparative analysis of Borrelia genomes to identify determinants of human pathogenicity.

• MeSH
• Borrelia burgdorferi komplex genetika   klasifikace   MeSH
• Borrelia burgdorferi genetika   klasifikace   MeSH
• Borrelia genetika   klasifikace   MeSH
• fylogeneze * MeSH
• genetická variace MeSH
• genom bakteriální * MeSH
• interakce mikroorganismu a hostitele genetika   MeSH
• klíště mikrobiologie   MeSH
• lidé MeSH
• lipoproteiny * genetika   MeSH
• lymeská nemoc * mikrobiologie   přenos   MeSH
• molekulární evoluce MeSH
• plazmidy genetika   MeSH
• rekombinace genetická * MeSH
• sekvenování celého genomu MeSH
• selekce (genetika) * MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Evropa MeSH
• Severní Amerika MeSH

V programu surveillance byl v roce 2023 zjištěn v České republice pokles počtu invazivních meningokokových onemocnění oproti předchozímu roku: celkem 16 (nemocnost 0,15/100 000 obyv.) proti 25 v roce 2022 (nemocnost 0,24/100000 obyv.). Z 16 onemocnění v roce 2023 jedno skončilo úmrtím – celková smrtnost 6,25 %. Toto úmrtí způsobila séroskupina Y ve věkové skupině nad 65 let věku. Podobně jako v předchozím roce převažovala i v roce 2023 onemocnění způsobená Neisseria meningitidis B (8 ze 16), čtyři onemocnění byla způsobená séroskupinou C a po jednom onemocnění způsobily séroskupiny A aY. U dvou případů nebyla séroskupina určena: N. meningitidis ND. V roce 2023 došlo ve srovnání s předchozím rokem k výraznému poklesu nemocnosti v nejmladší věkové skupině 0–11měsíčních (na 1,96/100 000 z 5,37/100000 obyv.). Nemocnost v nejmladší věkové skupině klesla u onemocnění způsobeného séroskupinou B (na 0,98/100 000 z 3,58/100000 obyv.) i u séroskupin preventabilních konjugovanou tetravakcínou A, C, W, Y (na 0,98/100 000 z 1,79/100000 obyv.). Ve věkové skupině 1–4letých nemocnost v roce 2023 mírně klesla oproti předchozímu roku (na 0,43/100 000 z 0,67/100000 obyv.) a byla způsobena pouze séroskupinou B. Ve věkové skupině 15–19 letých v roce 2023 nemocnost poklesla oproti předchozímu roku (na 0,18/100 000 z 0,79/100 000 obyv.) a byla rovněž způsobena pouze séroskupinou B. Z 16 invazivních meningokokových onemocnění v roce 2023 bylo 9 prokázáno pouze kultivačně, 2 kultivačně a metodou PCR, 5 pouze metodou PCR. V roce 2023 byla v Národní referenční laboratoři provedena multilokusová sekvenční typizace (MLST) u všech 9 kmenů z invazivního meningokokového onemocnění, které byly do NRL pro meningokokové nákazy poslány. MLST prokázala heterogenitu izolátů způsobujících IMO: celkem bylo zjištěno 5 hypervirulentních klonálních komplexů, z nich nejčastější byl cc103 (3 izoláty), následovaný cc11, cc213, cc23 a cc41/44 (vždy po jednom izolátu). MLST analýze byl podroben také jeden izolát od kontaktu s IMO s výsledkem cc103.

In the surveillance programme, a decrease in the number of invasive meningococcal diseases (IMD) was detected in the Czech Republic in 2023 compared to the previous year: a total of 16 (incidence 0.15/100000) compared to 25 in 2022 (incidence 0.24/100000). Of the 16 cases in 2023, one resulted in death – an overall case fatality rate was 6.25%. This death was caused by serogroup Y in the age group over 65 years. As in the previous year, Neisseria meningitidis B accounted for the majority of cases in 2023 (8 out of 16), four cases were caused by serogroup C and one case each by serogroups A and Y. In two cases, the serogroup was not determined: N. meningitidis ND. In 2023, there was a significant decrease in the morbidity in the youngest age group 0–11 months (to 1.96/100,000 from 5.37/100,000) compared to the previous year. Morbidity in the youngest age group decreased for serogroup B (to 0.98/100,000 from 3.58/100,000) and for serogroups preventable with conjugate tetravaccine A, C, W, Y (to 0.98/100,000 from 1.79/100,000). In the age group 1–4 years old, the morbidity in 2023 decreased slightly compared to the previous year (to 0.43/100,000 from 0.67/100,000) and was caused only by serogroup B. In the age group 15–19 years old, the morbidity in 2023 decreased compared to the previous year (to 0.18/100 000 from 0.79/100000) and was also due to serogroup B only. Of the 16 invasive meningococcal disease cases in 2023, 9 were proven by culture only, 2 by culture and PCR, and 5 by PCR only. In 2023, multilocus sequence typing (MLST) was performed for all the 9 strains from the invasive meningococcal disease cases sent to the National Reference Laboratory for Meningococcal Infections. MLST demonstrated heterogeneity of the isolates causing IMD: a total of 5 hypervirulent clonal complexes were identified, the most common being cc103 (3 isolates), followed by cc11, cc213, cc23 and cc41/44 (one isolate each). One isolate from the IMD contact was also subjected to MLST analysis with the result of cc103.

• MeSH
• lidé MeSH
• meningokokové infekce * epidemiologie   mortalita   prevence a kontrola   MeSH
• meningokokové vakcíny MeSH
• Neisseria meningitidis izolace a purifikace   klasifikace   MeSH
• polymerázová řetězová reakce MeSH
• séroskupina MeSH
• surveillance populace MeSH
• věkové rozložení MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• grafy a diagramy MeSH
• Geografické názvy
• Česká republika MeSH

Early identification of resistant cancer cells is currently a major challenge, as their expansion leads to refractoriness. To capture the dynamics of these cells, we made a comprehensive analysis of disease progression and treatment response in a chronic lymphocytic leukemia (CLL) patient using a combination of single-cell and bulk genomic methods. At diagnosis, the patient presented with unfavorable genetic markers, including notch receptor 1 (NOTCH1) mutation and loss(11q). The initial and subsequent treatment lines did not lead to a durable response and the patient developed refractory disease. Refractory CLL cells featured substantial dysregulation in B-cell phenotypic markers such as human leukocyte antigen (HLA) genes, immunoglobulin (IG) genes, CD19 molecule (CD19), membrane spanning 4-domains A1 (MS4A1; previously known as CD20), CD79a molecule (CD79A) and paired box 5 (PAX5), indicating B-cell de-differentiation and disease transformation. We described the clonal evolution and characterized in detail two cell populations that emerged during the refractory disease phase, differing in the presence of high genomic complexity. In addition, we successfully tracked the cells with high genomic complexity back to the time before treatment, where they formed a rare subpopulation. We have confirmed that single-cell RNA sequencing enables the characterization of refractory cells and the monitoring of their development over time.

• MeSH
• analýza jednotlivých buněk * metody   MeSH
• chemorezistence genetika   MeSH
• chronická lymfatická leukemie * genetika   patologie   MeSH
• lidé MeSH
• sekvenční analýza RNA MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• kazuistiky MeSH