263 results on '"Šmajs, David"'
Search Results
252. Bacterial but Not Fungal Gut Microbiota Alterations Are Associated With Common Variable Immunodeficiency (CVID) Phenotype.
- Author
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Fiedorová K, Radvanský M, Bosák J, Grombiříková H, Němcová E, Králíčková P, Černochová M, Kotásková I, Lexa M, Litzman J, Šmajs D, and Freiberger T
- Subjects
- Adult, Aged, Bacteria classification, Bacteria genetics, Biodiversity, Case-Control Studies, Common Variable Immunodeficiency immunology, Family Health, Feces microbiology, Female, Fungi classification, Fungi genetics, Health Status, Humans, Immunoglobulin A blood, Immunoglobulin A immunology, Male, Middle Aged, Bacteria immunology, Common Variable Immunodeficiency microbiology, Fungi immunology, Gastrointestinal Microbiome immunology, Mycobiome
- Abstract
Common Variable Immunodeficiency (CVID) is the most frequent symptomatic immune disorder characterized by reduced serum immunoglobulins. Patients often suffer from infectious and serious non-infectious complications which impact their life tremendously. The monogenic cause has been revealed in a minority of patients so far, indicating the role of multiple genes and environmental factors in CVID etiology. Using 16S and ITS rRNA amplicon sequencing, we analyzed the bacterial and fungal gut microbiota, respectively, in a group of 55 participants constituting of CVID patients and matched healthy controls including 16 case-control pairs living in the same household, to explore possible associations between gut microbiota composition and disease phenotype. We revealed less diverse and significantly altered bacterial but not fungal gut microbiota in CVID patients, which additionally appeared to be associated with a more severe disease phenotype. The factor of sharing the same household impacted both bacterial and fungal microbiome data significantly, although not as strongly as CVID diagnosis in bacterial assessment. Overall, our results suggest that gut bacterial microbiota is altered in CVID patients and may be one of the missing environmental drivers contributing to some of the symptoms and disease severity. Paired samples serving as controls will provide a better resolution between disease-related dysbiosis and other environmental confounders in future studies.
- Published
- 2019
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253. Directly Sequenced Genomes of Contemporary Strains of Syphilis Reveal Recombination-Driven Diversity in Genes Encoding Predicted Surface-Exposed Antigens.
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Grillová L, Oppelt J, Mikalová L, Nováková M, Giacani L, Niesnerová A, Noda AA, Mechaly AE, Pospíšilová P, Čejková D, Grange PA, Dupin N, Strnadel R, Chen M, Denham I, Arora N, Picardeau M, Weston C, Forsyth RA, and Šmajs D
- Abstract
Syphilis, caused by Treponema pallidum subsp. pallidum (TPA), remains an important public health problem with an increasing worldwide prevalence. Despite recent advances in in vitro cultivation, genetic variability of this pathogen during infection is poorly understood. Here, we present contemporary and geographically diverse complete treponemal genome sequences isolated directly from patients using a methyl-directed enrichment prior to sequencing. This approach reveals that approximately 50% of the genetic diversity found in TPA is driven by inter- and/or intra-strain recombination events, particularly in strains belonging to one of the defined genetic groups of syphilis treponemes: Nichols-like strains. Recombinant loci were found to encode putative outer-membrane proteins and the recombination variability was almost exclusively found in regions predicted to be at the host-pathogen interface. Genetic recombination has been considered to be a rare event in treponemes, yet our study unexpectedly showed that it occurs at a significant level and may have important impacts in the biology of this pathogen, especially as these events occur primarily in the outer membrane proteins. This study reveals the existence of strains with different repertoires of surface-exposed antigens circulating in the current human population, which should be taken into account during syphilis vaccine development.
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- 2019
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254. Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue.
- Author
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Knauf S, Gogarten JF, Schuenemann VJ, De Nys HM, Düx A, Strouhal M, Mikalová L, Bos KI, Armstrong R, Batamuzi EK, Chuma IS, Davoust B, Diatta G, Fyumagwa RD, Kazwala RR, Keyyu JD, Lejora IAV, Levasseur A, Liu H, Mayhew MA, Mediannikov O, Raoult D, Wittig RM, Roos C, Leendertz FH, Šmajs D, Nieselt K, Krause J, and Calvignac-Spencer S
- Subjects
- Africa South of the Sahara epidemiology, Animals, Female, Humans, Male, Phylogeny, Primate Diseases epidemiology, Primates, Treponema pallidum genetics, Treponema pallidum physiology, Yaws epidemiology, Yaws microbiology, Primate Diseases microbiology, Treponema pallidum isolation & purification, Yaws veterinary
- Published
- 2018
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255. Colicin F Y inhibits pathogenic Yersinia enterocolitica in mice.
- Author
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Bosák J, Micenková L, Hrala M, Pomorská K, Kunova Bosakova M, Krejci P, Göpfert E, Faldyna M, and Šmajs D
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- Animals, DNA, Recombinant genetics, Escherichia coli genetics, Escherichia coli metabolism, Escherichia coli physiology, Intestines microbiology, Mice, Colicins metabolism, Yersinia enterocolitica physiology
- Abstract
Yersiniosis belongs to the common foodborne diseases around the world, and frequently manifests as diarrhea that can be treated with probiotics. Colicin F
Y is an antibacterial agent produced by bacteria and it is capable of specific growth inhibition of Yersinia enterocolitica, the causative agent of gastrointestinal yersiniosis. In this study, recombinant E. coli producing colicin FY were constructed, using both known probiotic strains EcH22 and EcColinfant, and the newly isolated murine strains Ec1127 and Ec1145. All E. coli strains producing colicin FY inhibited growth of pathogenic Y. enterocolitica during co-cultivation in vitro. In dysbiotic mice treated with streptomycin, E. coli strains producing colicin FY inhibited progression of Y. enterocolitica infections. This growth inhibition was not observed in mice with normal gut microflora, likely due to insufficient colonization capacity of E. coli strains and/or due to spatial differences in intestinal niches. Isogenic Y. enterocolitica producing colicin FY was constructed and shown to inhibit pathogenic Y. enterocolitica in mice with normal microflora. Evidence of in vivo antimicrobial activity of colicin FY may have utility in the treatment of Y. enterocolitica infections.- Published
- 2018
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256. Escherichia coli isolates from patients with inflammatory bowel disease: ExPEC virulence- and colicin-determinants are more frequent compared to healthy controls.
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Micenková L, Frankovičová L, Jaborníková I, Bosák J, Dítě P, Šmarda J, Vrba M, Ševčíková A, Kmeťová M, and Šmajs D
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- Bacterial Toxins genetics, Electrophoresis, Gel, Pulsed-Field, Escherichia coli genetics, Escherichia coli metabolism, Escherichia coli Proteins genetics, Extraintestinal Pathogenic Escherichia coli isolation & purification, Fimbriae Proteins genetics, Humans, Oxo-Acid-Lyases genetics, Bacteriocins metabolism, Colitis, Ulcerative microbiology, Crohn Disease microbiology, Escherichia coli isolation & purification, Extraintestinal Pathogenic Escherichia coli pathogenicity, Gastrointestinal Microbiome physiology
- Abstract
A set of 178 Escherichia coli isolates taken from patients with inflammatory bowel disease (IBD) was analyzed for bacteriocin production and tested for the prevalence of 30 bacteriocin and 22 virulence factor determinants. Additionally, E. coli phylogenetic groups were also determined. Pulsed-field gel electrophoresis (PFGE) was used for exclusion of clonal character of isolates. Results were compared to data from a previously published analysis of 1283 fecal commensal E. coli isolates. The frequency of bacteriocinogenic isolates (66.9%) was significantly higher in IBD E. coli compared to fecal commensal E. coli isolates (54.2%, p < 0.01). In the group of IBD E. coli isolates, a higher prevalence of determinants for group B colicins (i.e., colicins B, D, Ia, Ib, M, and 5/10) (p < 0.01), including a higher prevalence of the colicin B determinant (p < 0.01) was found. Virulence factor determinants encoding fimbriae (fimA, 91.0%; pap, 27.5%), cytotoxic necrotizing factor (cnf1, 11.2%), aerobactin synthesis (aer, 43.3%), and the locus associated with invasivity (ial, 9.0%) were more prevalent in IBD E. coli (p < 0.05 for all five determinants). E. coli isolates from IBD mucosal biopsies were more frequently bacteriocinogenic (84.6%, p < 0.01) compared to fecal IBD isolates and fecal commensal E. coli. PFGE analysis revealed clusters specific for IBD E. coli isolates (n = 11), for fecal isolates (n = 13), and clusters containing both IBD and fecal isolates (n = 10). ExPEC (Extraintestinal Pathogenic E. coli) virulence and colicin determinants appear to be important characteristics of IBD E. coli isolates, especially the E. coli isolates obtained directly from biopsy samples., (Copyright © 2018 Elsevier GmbH. All rights reserved.)
- Published
- 2018
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257. Isolated populations of Ixodes lividus ticks in the Czech Republic and Belgium host genetically homogeneous Rickettsia vini.
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Nováková M, Heneberg P, Heylen DJA, Medvecký M, Muñoz-Leal S, Šmajs D, and Literák I
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- Animals, Belgium epidemiology, Biological Coevolution genetics, Bird Diseases microbiology, Birds parasitology, Czech Republic epidemiology, DNA, Bacterial genetics, Humans, Likelihood Functions, Nymph, Phylogeny, Rickettsia classification, Rickettsia isolation & purification, Rickettsia Infections epidemiology, Rickettsia Infections microbiology, Spotted Fever Group Rickettsiosis epidemiology, Spotted Fever Group Rickettsiosis microbiology, Tick Infestations epidemiology, Argasidae microbiology, Ixodes microbiology, Rickettsia genetics, Rickettsia Infections veterinary, Spotted Fever Group Rickettsiosis veterinary, Tick Infestations veterinary
- Abstract
In the last two decades, the advent of molecular methods has revealed a remarkable diversity of rickettsiae (Rickettsiales: Rickettsiaceae) in invertebrates. Several species of these obligate intracellular bacteria are known to cause human infections, hence more attention has been directed towards human-biting ectoparasites. A spotted fever group Rickettsia sp. was previously detected in Ixodes lividus ticks (Ixodidae) associated with sand martins (Hirundinidae: Riparia riparia). In order to identify whether this rickettsia varies among isolated tick populations, a total of 1758 I. lividus ticks and five Ixodes ricinus ticks (Ixodidae) were collected in the Czech Republic and 148 I. lividus ticks were collected in Belgium, from nests of sand martins, European bee-eaters (Meropidae: Merops apiaster), Eurasian tree sparrows (Passeridae: Passer montanus), and from captured sand martins. We screened 165 and 78 I. lividus ticks (from the Czech Republic and Belgium, respectively) and all five I. ricinus ticks for the presence of rickettsial DNA. Only I. lividus samples were positive for Rickettsia vini, a spotted fever group rickettsia that commonly infects the tree-hole tick Ixodes arboricola (Ixodidae). Maximum likelihood analysis of the rickettsial sequences showed that the most closely related organism to R. vini corresponds to an uncharacterized rickettsia detected in Argas lagenoplastis (Argasidae), a nidicolous soft tick of the fairy martin (Hirundinidae: Petrochelidon ariel) in Australia. The observed variability of R. vini sequences from isolated tick populations was low; all 85 sequenced samples were identical to each other in five out of six partial rickettsial genes, except for the sca4 sequence (99.9% identity, 808/809 nt) that differed in I. lividus ticks from two sampling sites in the Czech Republic., (Copyright © 2018 Elsevier GmbH. All rights reserved.)
- Published
- 2018
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258. Human Escherichia coli isolates from hemocultures: Septicemia linked to urogenital tract infections is caused by isolates harboring more virulence genes than bacteraemia linked to other conditions.
- Author
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Micenková L, Beňová A, Frankovičová L, Bosák J, Vrba M, Ševčíková A, Kmeťová M, and Šmajs D
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, Colicins genetics, Electrophoresis, Gel, Pulsed-Field, Escherichia coli classification, Escherichia coli genetics, Female, Gastroenteritis complications, Genotype, Humans, Infant, Male, Middle Aged, Neoplasms complications, Phylogeny, Urinary Tract Infections complications, Young Adult, Escherichia coli isolation & purification, Escherichia coli pathogenicity, Escherichia coli Infections microbiology, Sepsis microbiology, Virulence Factors genetics
- Abstract
Escherichia coli is the most common cause of bloodstream infections and community-acquired sepsis. The main aim of this study was to determine virulence characteristics of E. coli isolates from hemocultures of patients with a primary disease of urogenital tract, digestive system, a neoplastic blood disease, or other conditions. Results from a set of 314 E. coli isolates from hemocultures were compared to data from a previously published analysis of 1283 fecal commensal E. coli isolates. Genetic profiling of the 314 E. coli isolates involved determination of phylogenetic group (A, B1, B2, D, C, E, and F), identification of 21 virulence factors, as well as 30 bacteriocin-encoding determinants. Pulsed-field gel electrophoresis was used to analyze clonal character of the hemoculture-derived isolates. The E. coli isolates from hemocultures belonged mainly to phylogenetic groups B2 (59.9%) and D (21.0%), and less frequently to phylogroups A (10.2%) and B1 (5.7%). Commonly detected virulence factors included adhesins (fimA 92.0%, pap 47.1%, and sfa 26.8%), and iron-uptake encoding genes (fyuA 87.9%, fepC 79.6%, aer 70.7%, iucC 68.2%, and ireA 13.7%), followed by colibactin (pks island 31.5%), and cytotoxic necrotizing factor (cnf1 11.1%). A higher frequency of microcin producers (and microcin M determinant) and a lower frequency of colicin Ib and microcin B17 was found in hemoculture-derived isolates compared to commensal fecal isolates. E. coli isolates from hemocultures harbored more virulence genes compared to fecal E. coli isolates. In addition, hemoculture E. coli isolates from patients with primary diagnosis related to urogenital tract were clearly different and more virulence genes were detected in these isolates compared to both fecal isolates and hemoculture-derived isolates from patients with blood and gastrointestinal diseases., (Copyright © 2017 Elsevier GmbH. All rights reserved.)
- Published
- 2017
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259. Colicins U and Y inhibit growth of Escherichia coli strains via recognition of conserved OmpA extracellular loop 1.
- Author
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Bosák J, Micenková L, Doležalová M, and Šmajs D
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- Bacterial Outer Membrane Proteins genetics, DNA Mutational Analysis, Escherichia coli genetics, Female, Humans, Male, Microbial Sensitivity Tests, Protein Binding, Serratia marcescens genetics, Bacterial Outer Membrane Proteins metabolism, Colicins metabolism, Escherichia coli drug effects, Escherichia coli growth & development
- Abstract
Interactions of colicins U and Y with the OmpA (Outer membrane protein A) receptor molecule were studied using site-directed mutagenesis and colicin binding assay. A systematic mutagenesis of the colicin-susceptible OmpA sequence from Escherichia coli (OmpA
EC ) to the colicin-resistant OmpA sequence from Serratia marcescens (OmpASM ) was performed in regions corresponding to extracellular OmpA loops 1-4. Susceptibility to colicins U and Y was significantly affected by the OmpA mutation in loop 1. As with functional analysis, a decrease in binding capacity of His-tagged colicin U was found for recombinant OmpA with a mutated segment in loop 1 compared to control OmpAEC . To verify the importance of the identified amino acid residues in OmpA loop 1, we introduced loop 1 from OmpAEC into OmpASM , which resulted in the substantial increase of susceptibility to colicins U and Y. In addition, colicins U and Y were tested against a panel of 118 bacteriocin non-producing strains of four Escherichia species, including E. coli (39 strains), E. fergusonii (10 strains), E. hermannii (42 strains), and E. vulneris (27 strains). A majority (82%) of E. coli strains was susceptible to colicins U and Y. Interestingly, colicins U and Y also inhibited all of the 30 tested multidrug-resistant E. coli O25b-ST131 isolates. These findings, together with the fact that OmpA loop 1 is important for bacterial virulence and is evolutionary conserved, offer the potential of using colicins U and Y as specific anti-OmpA loop 1 directed antibacterial proteins., (Copyright © 2016 Elsevier GmbH. All rights reserved.)- Published
- 2016
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260. The 2 simultaneously published "k" sequence variants of tp0548 locus of Treponema pallidum ssp. pallidum isolates differ: the one published later has to be renamed as "l".
- Author
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Grillová L, Strouhal M, Mikalová L, and Šmajs D
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- Female, Humans, Male, Molecular Typing, Syphilis epidemiology, Syphilis microbiology, Treponema pallidum classification, Treponema pallidum genetics
- Published
- 2015
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261. Structure of rrn operons in pathogenic non-cultivable treponemes: sequence but not genomic position of intergenic spacers correlates with classification of Treponema pallidum and Treponema paraluiscuniculi strains.
- Author
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Čejková D, Zobaníková M, Pospíšilová P, Strouhal M, Mikalová L, Weinstock GM, and Šmajs D
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- Base Sequence, DNA, Bacterial chemistry, DNA, Bacterial genetics, Genetic Variation, Genome, Bacterial, Genotype, Molecular Sequence Data, Phylogeny, Sequence Analysis, DNA, Sequence Deletion, DNA, Ribosomal Spacer genetics, RNA, Ribosomal, 16S genetics, RNA, Ribosomal, 23S genetics, Treponema pallidum classification, Treponema pallidum genetics, rRNA Operon
- Abstract
This study examined the sequences of the two rRNA (rrn) operons of pathogenic non-cultivable treponemes, comprising 11 strains of T. pallidum ssp. pallidum (TPA), five strains of T. pallidum ssp. pertenue (TPE), two strains of T. pallidum ssp. endemicum (TEN), a simian Fribourg-Blanc strain and a rabbit T. paraluiscuniculi (TPc) strain. PCR was used to determine the type of 16S-23S ribosomal intergenic spacers in the rrn operons from 30 clinical samples belonging to five different genotypes. When compared with the TPA strains, TPc Cuniculi A strain had a 17 bp deletion, and the TPE, TEN and Fribourg-Blanc isolates had a deletion of 33 bp. Other than these deletions, only 17 heterogeneous sites were found within the entire region (excluding the 16S-23S intergenic spacer region encoding tRNA-Ile or tRNA-Ala). The pattern of nucleotide changes in the rrn operons corresponded to the classification of treponemal strains, whilst two different rrn spacer patterns (Ile/Ala and Ala/Ile) appeared to be distributed randomly across species/subspecies classification, time and geographical source of the treponemal strains. It is suggested that the random distribution of tRNA genes is caused by reciprocal translocation between repetitive sequences mediated by a recBCD-like system.
- Published
- 2013
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262. Sequencing-based molecular typing of treponema pallidum strains in the Czech Republic: all identified genotypes are related to the sequence of the SS14 strain.
- Author
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Flasarová M, Pospíšilová P, Mikalová L, Vališová Z, Dastychová E, Strnadel R, Kuklová I, Woznicová V, Zákoucká H, and Šmajs D
- Subjects
- Adult, Anti-Bacterial Agents therapeutic use, Base Sequence, Czech Republic epidemiology, Drug Resistance, Bacterial genetics, Female, Genetic Variation, Genotype, Humans, Male, Molecular Sequence Data, Phenotype, Polymerase Chain Reaction, Sequence Analysis, DNA, Syphilis diagnosis, Syphilis drug therapy, Syphilis epidemiology, Treponema pallidum drug effects, Treponema pallidum immunology, DNA, Bacterial analysis, RNA, Ribosomal, 23S genetics, Ribotyping methods, Syphilis microbiology, Treponema pallidum genetics
- Abstract
A set of 415 clinical samples isolated from 294 patients suspected of having syphilis collected in the Czech Republic between 2004 and 2010 was tested for the presence of treponemal DNA. Standard serological tests showed that 197 patients were syphilis-seropositive and 97 patients were syphilis-seronegative. In each sample, PCR tests for polA (TP0105), tmpC (TP0319), TP0136, TP0548 and 23S rRNA genes were performed. Samples taken from 91 patients were PCR-positive. Molecular typing of treponemal DNA was based on the sequencing of TP0136, TP0548 and 23S rRNA genes. Treponemal DNA was typeable in samples taken from 64 PCR-positive patients and 9 different genotypes were found. The proportion of treponemal strains resistant to macrolide antibiotics was 37.3%. In the DNA samples taken from 39 patients, a parallel treponemal typing approved by Centers for Disease Control and Prevention was performed. The variants of arp and tpr genes appear to combine independently with sequence variants of TP0136, TP0548 and 23S rRNA genes.
- Published
- 2012
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263. Macrolide treatment failure in a case of secondary syphilis: a novel A2059G mutation in the 23S rRNA gene of Treponema pallidum subsp. pallidum.
- Author
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Matějková P, Flasarová M, Zákoucká H, Bořek M, Křemenová S, Arenberger P, Woznicová V, Weinstock GM, and Šmajs D
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- Adolescent, Adult, Animals, Child, Child, Preschool, Czech Republic epidemiology, DNA, Bacterial analysis, DNA, Bacterial isolation & purification, Humans, Infant, Infant, Newborn, Macrolides pharmacology, Macrolides therapeutic use, Male, Middle Aged, Prevalence, Rabbits, Sequence Analysis, DNA, Syphilis epidemiology, Syphilis microbiology, Treatment Failure, Treponema pallidum genetics, Young Adult, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents therapeutic use, Drug Resistance, Bacterial genetics, Mutation, RNA, Ribosomal, 23S genetics, Spiramycin pharmacology, Spiramycin therapeutic use, Syphilis drug therapy, Treponema pallidum drug effects
- Abstract
We report an occurrence of treatment failure after oral spiramycin therapy in a man with secondary syphilis and a reported penicillin and tetracycline allergy. Molecular detection revealed treponemal DNA in the blood of the patient and sequencing of the 23S rDNA identified an A to G transition at the gene position corresponding to position 2059 in the Escherichia coli 23S rRNA gene. The occurrence of this novel 23S rDNA mutation was examined among 7 rabbit-propagated syphilitic strains of Treponema pallidum and among 22 syphilis patient isolates from the Czech Republic. The prevalence of A2058G and A2059G mutations among clinical specimens was 18.2 and 18.2 %, respectively.
- Published
- 2009
- Full Text
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