Jsou prezentovány první výsledky charakterizace kmenů Haemophilus influenzae novou metodoumultilokusové sekvenační typizace (MLST). Charakterizace souboru 28 kmenů H. influenzae izolovanýchz invazivních onemocnění v České republice ukázala klonální homogenitu těchto kmenů:z 26 testovaných kmenů H. influenzae b vykazovalo 22 kmenů jednotný sekvenční typ: ST-6. U 4kmenů byly zjištěny námi nově popsané sekvenční typy: ST-83 (3 kmeny) a ST-84 (1 kmen). U 2netypovatelných kmenů H. influenzae byly zjištěny jiné sekvenční typy než ST-6: ST-3 a námi nověpopsaný ST-85. První výsledky MLST ukazují, že ST-6 je typický pro H. influenzae b izolovanéz invazivních onemocnění v České republice. Námi nově popsané sekvenční typy ST-83, ST-84 a ST-85byly registrovány v celosvětové databázi MLST H. influenzae (http://haemophilus.mlst.net).
First results of multilocus sequence typing (MLST) of Haemophilus influenzae strains are presented.MLST of 28 H. influenzae strains isolated frompatients with invasive diseases in the Czech Republicis indicative of clonal homogeneity of these strains: 22 out of 26 H. influenzae b strains tested wereof the same sequence type, ST-6. Four strains were of two sequence types newly described in thisstudy: ST-83 (3 strains) and ST-84 (1 strain). Two nontypeable H. influenzae strains were assigned tosequence types other than ST-6: ST-3 and ST-85 newly described in this study. First MLST resultsshow ST-6 to be typical of H. influenzae b isolated from patients with invasive diseases in the CzechRepublic. The sequence types newly described in this study, i.e. ST-83, ST-84 and ST-85, weresubmitted to the worldwide H. influenzae MLST database (http://haemophilus.mlst.net).
- MeSH
- Clone Cells MeSH
- Research Support as Topic MeSH
- Haemophilus influenzae genetics pathogenicity MeSH
- Humans MeSH
- Polymerase Chain Reaction MeSH
- Base Sequence MeSH
- Serotyping methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Database MeSH
- Review MeSH
- Comparative Study MeSH
Telomeres are nucleoprotein structures that distinguish native chromosomal ends from double-stranded breaks. They are maintained by telomerase that adds short G-rich telomeric repeats at chromosomal ends in most eukaryotes and determines the TnAmGo sequence of canonical telomeres. We employed an experimental approach that was based on detection of repeats added by telomerase to identify the telomere sequence type forming the very ends of chromosomes. Our previous studies that focused on the algal order Chlamydomonadales revealed several changes in telomere motifs that were consistent with the phylogeny and supported the concept of the Arabidopsis-type sequence being the ancestral telomeric motif for green algae. In addition to previously described independent transitions to the Chlamydomonas-type sequence, we report that the ancestral telomeric motif was replaced by the human-type sequence in the majority of algal species grouped within a higher order clade, Caudivolvoxa. The Arabidopsis-type sequence was apparently retained in the Polytominia clade. Regarding the telomere sequence, the Chlorogonia clade within Caudivolvoxa bifurcates into two groups, one with the human-type sequence and the other group with the Arabidopsis-type sequence that is solely formed by the Chlorogonium species. This suggests that reversion to the Arabidopsis-type telomeric motif occurred in the common ancestral Chlorogonium species. The human-type sequence is also synthesized by telomerases of algal strains from Arenicolinia, Dunaliellinia and Stephanosphaerinia, except a distinct subclade within Stephanosphaerinia, where telomerase activity was not detected and a change to an unidentified telomeric motif might arise. We discuss plausible reasons why changes in telomeric motifs were tolerated during evolution of green algae.
- MeSH
- Amino Acid Motifs genetics MeSH
- Phylogeny MeSH
- Repetitive Sequences, Nucleic Acid genetics MeSH
- DNA, Ribosomal genetics MeSH
- RNA, Ribosomal, 18S genetics MeSH
- Base Sequence MeSH
- Sequence Analysis, DNA MeSH
- Telomerase genetics MeSH
- Telomere genetics MeSH
- Volvocida genetics MeSH
- Telomere Shortening genetics MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
BACKGROUND: The resistance of Streptococcus pneumoniae to macrolides is becoming an increasingly important issue and thus it is important to understand the genetics related to adaptation of this species to the widespread use of antibiotics in Europe. The 58 isolates of S. pneumoniae belonging to sequence type (ST) 416 and serotype 19A and to several different phenotypes originated from Italy, Portugal and Czech Republic were thus sequenced on Illumina MiSeq. The aim of the study was to describe genetical origine of isolates, investigate their macrolide resistance and suggest reasons for spread of ST416 in the Czech Republic. RESULTS: Investigation of genes associated with serotype determined serotype switch between 15B and 19A serotypes and core genome multilocus sequence typing (cgMLST) confirmed the origine of concerned isolates in Netherlands15B-37 clone. Inspected genomes proved variability of genes associated with the macrolide resistance even within closely genetically relative isolates. CONCLUSIONS: Participation of 19A/ST416 on the spread of Netherlands15B-37 is accompanied by serotype switch between 19A and 15B serotypes and with acquisition of genes involved in macrolide resistance to the clone that was originally macrolide susceptible. There is evident tendency to interchanging and modifications of these and surrounding genes, that could lead to accelerate spreading of this sequence type in regions with high macrolide consumption.
- MeSH
- Drug Resistance, Bacterial * MeSH
- Phylogeny MeSH
- Phylogeography MeSH
- Genome, Bacterial MeSH
- Polymorphism, Single Nucleotide MeSH
- Humans MeSH
- Macrolides pharmacology MeSH
- Multilocus Sequence Typing MeSH
- Pneumococcal Infections microbiology MeSH
- Whole Genome Sequencing methods MeSH
- Serogroup MeSH
- Streptococcus pneumoniae classification drug effects genetics isolation & purification MeSH
- High-Throughput Nucleotide Sequencing MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czech Republic MeSH
- Italy MeSH
- Netherlands MeSH
- Portugal MeSH
V článku jsou prezentovány první výsledky charakterizace 29 invazivních kmenů Streptococcuspyogenes, izolovaných v České republice v první polovině roku 2003, metodou multilokusové sekvenačnítypizace (MLST). U žádného z 16 přítomných emm typů nebyla mezi kmeny našeho souboruzjištěna variabilita sekvenčních typů (ST). První výsledky MLST ukazují, že populace kmenůzpůsobujících závažná onemocnění v České republice je odlišná od kmenů izolovaných v zahraničí.U sedmi kmenů byly popsány nové sekvenční typy: ST134, ST308, ST336, 5T340, obsahující novékombinace známých alel a ST341 se třemi dosud nepopsanými alelami (gki 91, murI 65 a yqiL 60),zjištěný u třech kmenů. Nově popsané sekvenční typy byly registrovány v celosvětové databáziMLST S. pyogenes.
First results of multilocus sequence typing (MLST) for characterization of 29 invasive Streptococcuspyogenes strains isolated in the Czech Republic in the first half of 2003 are presented. None of 16emm types detected among the study strains showed sequence type (ST) variability. The MLSTresults are indicative of differences between the strains causing serious diseases in the CzechRepublic and those isolated in other countries. In seven strains, four new STs with known alleles innew combinations, ST134, ST308, ST336, ST340, and one new ST with three as yet undescribed alleles(gki 91, murI 65 and yqiL 60), ST341, were described. These newly described STs were submitted tothe web-based reference MLST database for S. pyogenes.
- MeSH
- Alleles MeSH
- Research Support as Topic MeSH
- Cloning, Molecular MeSH
- Humans MeSH
- Sequence Analysis MeSH
- Streptococcus pyogenes isolation & purification classification pathogenicity MeSH
- Check Tag
- Humans MeSH
- Publication type
- Database MeSH
- Review MeSH
- Comparative Study MeSH
- Geographicals
- Czech Republic MeSH
The foot and mouth disease virus (FMDV) causes a vesicular and contagious disease of cloven-hoofed animals. In this study, the virus was isolated from vesicles of the infected cattle using cell culture and serotyped by ELISA test. The extracted RNA from the infected cells was reverse transcribed and amplified using VP1 gene-specific primer pairs by means of one-step RT-PCR. The purified VP1 gene was sub-cloned into the uniqe KpnI and BamHI cloning sites of the pcDNA3.1+ vector. The DH5α strain of E. coli was transformed by the vector. The sequences of sub-cloned FMDV type O/IRN/2007 VP1 were aligned with FMDV type O/UKG/2001 VP1 using MegAlign software. Nucleotide sequence comparisons were made using the BLAST software available from the NCBI website. The amino acid sequences of three sub-cloned FMDV type O/IRN/2007 VP1 were also aligned with three other similar sequences using MegAlign software. Nineteen of the most similar VP1 nucleotide sequences (by BLASTN program), FMDV O/IRN/2007 VP1 sequence, twenty isolates of FMDV-O VP1 in Iran and eight topotypes of FMDV type O were aligned by Mega5 to create a FMDV-O VP1-based sequence similarity tree. The nucleotide sequence comparison indicated that FMDV O/ IRN/2007 VP1 had the greatest nucleotide sequence similarity to the VP1 gene of FMDV O1/Manisa/Turkey/69 (99%), FMDV O1/Manisa/Netherlands (98%) and FMDV O1/Manisa/iso87/Turkey (98%). It was also observed that the highest identity between FMDV O/IRN/2007 VP1 sequence and other nucleotide sequences of FMDV type O VP1 genes isolated in Iran during 1997-2004 was about 91%.
- MeSH
- Phylogeny MeSH
- Molecular Sequence Data MeSH
- Amino Acid Sequence MeSH
- Base Sequence MeSH
- Sequence Analysis, DNA * MeSH
- Sequence Homology, Nucleic Acid MeSH
- Sequence Alignment MeSH
- Cattle MeSH
- Sus scrofa MeSH
- Genes, Viral genetics MeSH
- Capsid Proteins chemistry genetics MeSH
- Foot-and-Mouth Disease Virus genetics isolation & purification MeSH
- Animals MeSH
- Check Tag
- Cattle MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Iran MeSH
The strain Clostridium pasteurianum NRRL B-598 is non-type, oxygen tolerant, spore-forming, mesophilic and heterofermentative strain with high hydrogen production and ability of acetone-butanol fermentation (ethanol production being negligible). Here, we present the annotated complete genome sequence of this bacterium, replacing the previous draft genome assembly. The genome consisting of a single circular 6,186,879 bp chromosome with no plasmid was determined using PacBio RSII and Roche 454 sequencing.
Cíl: Klonální analýza metodou multilokusové sekvenční typizace (MLST) rozsáhlého souboru kmenů Haemophilus influenzae izolovaných z invazivního i neinvazivního onemocnění v České republice v letech 2001–2009. Materiál a metody: Metodou MLST bylo testováno 207 kmenů H. influenzae, z toho bylo 153 H. influenzae b (Hib), 2 H. influenzae e, 2 H. influenzae f a 50 neopouzdřených H. influenzae (HiNT). Výsledky: Při charakterizaci 153 Hib bylo zjištěno, že 73 % kmenů vykazuje sekvenční typ (ST) ST-6 a 15 % příbuzný ST-83. Další sekvenční typy byly zjištěny jen ojediněle (ST-92, ST-95, ST-108, ST-190, ST-326). Bylo zjištěno 5 nových ST (ST-663 až ST-667). Všechny ST zjištěné u Hib náležely do klonálního komplexu cc6. Metodou MLST bylo testováno 12 kmenů izolovaných z klinického materiálu u skutečného selhání Hib vakcíny: 9 kmenů vykazovalo ST-6, 2 kmeny ST-83 a jeden kmen ST-190. Izoláty H. influenzae e vykazovaly ST-18 a izoláty H. influenzae f vykazovaly ST-124. Jeden kmen HiNT izolovaný z likvoru vykazoval ST-6 typický pro Hib. U tohoto kmenu se zřejmě jedná o Hib, který ztratil schopnost tvořit pouzdro. Charakterizace dalších 49 testovaných kmenů HiNT vykazovalo 37 různých ST, nejčastěji zastoupený byl ST-276 (4 kmeny), ST-556 (3 kmeny), další ST se vyskytovaly jen ojediněle. Bylo zjištěno 9 nových ST (ST-668 až ST-676). Sekvenční typy H. influenzae non-b jsou heterogenní a nenáleží do klonálního komplexu cc6. Závěr: Populace českých izolátů Hib je velmi homogenní a všech 12 zjištěných ST náleží do jediného klonálního komplexu cc6. Sekvenční typ ST-6 je u Hib centrálním genotypem komplexu definovaného pomocí MLST a lze ho nazvat klonálním komplexem cc6. Zjištěné příbuzné varianty centrálního ST-6 jsou jednolokusovými variantami v rámci komplexu cc6 (ST-83, ST-92, ST-95, ST-108, ST-190, ST-326, ST-663 až ST-667). U všech případů selhání vakcíny byl zjištěn klonální komplex cc6. Populace H. influenzae non-b je velmi heterogenní a žádný z 39 zjištěných ST nenáleží do klonálního komplexu cc6.
Objective: Multilocus sequence typing (MLST)-based clonal analysis of a large set of Haemophilus influenzae strains isolated from both invasive and non-invasive cases in the Czech Republic in 2001–2009. Material and methods: A total of 207 H. influenzae strains, i. e. 153 H. influenzae b (Hib) strains, 2 H. influenzae e strains, 2 H. influenzae f strains and 50 non-capsulated H. influenzae (HiNT) strains, were tested by the MLST method. Results: MLST classified 73% of 153 Hib strains to sequence type (ST) ST-6 and 15% of them to related ST-83. Other sequence types were uncommon (ST-92, ST-95, ST-108, ST-190 and ST-326). Five new STs were found (ST-663 to ST-667). All STs observed in Hib strains belonged to clonal complex cc6. Of 12 strains isolated from clinical specimens of actual Hib vaccine failure cases, nine were classified by MLST into ST-6, two into ST-83 and one into ST-190. The H. influenzae type e isolates were of ST-18 while H. influenzae type f isolates belonged to ST-124. A HiNT strain isolated from the cerebrospinal fluid was of ST-6, typical of Hib, and may be a Hib strain that lost the capsule-forming ability. Characterization of other 49 HiNT strains revealed 37 different STs, with ST-276 being the most common (4 strains), followed by ST-556 (3 strains); other STs were only found sporadically. Nine new STs were identified (ST-668 to ST-676). STs of H. influenzae non-b are heterogeneous and do not belong to complex cc6. Conclusion: The population of the Czech Hib isolates is highly homogeneous and all 12 STs detected are members of the same clonal complex, cc6. ST-6 is the central genotype in Hib strains of MLST complex cc6. The detected ST-6 single-locus variants are from clonal complex cc6 (ST-83, ST-92, ST-95, ST-108, ST-190, ST-326, ST-663 to ST-667). Clonal complex cc6 was found in all vaccine failure cases. The population of H. influenzae non-b is highly heterogeneous and none of the 39 STs found matches clonal complex cc6.
- Keywords
- MLST, klonální analýza,
- MeSH
- Child MeSH
- Haemophilus influenzae genetics isolation & purification pathogenicity MeSH
- Culture Media diagnostic use MeSH
- Humans MeSH
- Molecular Epidemiology MeSH
- Multilocus Sequence Typing MeSH
- Sequence Analysis, DNA methods utilization MeSH
- Bacterial Typing Techniques standards utilization MeSH
- Check Tag
- Child MeSH
- Humans MeSH
A cosmid bearing an insert of 38 217 bp covering the gene cluster and its flanking regions of type strain Streptomyces lincolnensis ATCC 25466 was sequenced. Two relatively extensive sequence changes and several hundred point mutations were identified if compared with the previously published sequence of the lincomycin (Lin) industrial strain S. lincolnensis 78-11. Analysis of the cluster-flanking regions revealed its localization within the genome of the ATCC 25466 strain. The cluster-bearing cosmid was integrated into the chromosome of Lin non-producing strains S. coelicolor CH 999 and S. coelicolor M 145. The modified strains heterologously produced Lin but the level dropped to approximately 1-3% of the production in the ATCC 25466 strain.
- MeSH
- Anti-Bacterial Agents biosynthesis chemistry MeSH
- Bacterial Proteins genetics metabolism MeSH
- Biotechnology MeSH
- Point Mutation MeSH
- Gene Library MeSH
- Cosmids MeSH
- Lincomycin biosynthesis chemistry MeSH
- Multigene Family MeSH
- Sequence Analysis, DNA MeSH
- Streptomyces coelicolor genetics metabolism MeSH
- Streptomyces genetics metabolism growth & development MeSH
