Evaluation of 16S rRNA primer sets for characterisation of microbiota in paediatric patients with autism spectrum disorder.

intestinal microbiota is becoming a significant marker that reflects differences between health and disease status also in terms of gut-brain axis communication. Studies show that children with autism spectrum disorder (ASD) often have a mix of gut microbes that is distinct from the neurotypical children. Various assays are being used for microbiota investigation and were considered to be universal. However, newer studies showed that protocol for preparing DNA sequencing libraries is a key factor influencing results of microbiota investigation. The choice of DNA amplification primers seems to be the crucial for the outcome of analysis. In our study, we have tested 3 primer sets to investigate differences in outcome of sequencing analysis of microbiota in children with ASD. We found out that primers detected different portion of bacteria in samples especially at phylum level; significantly higher abundance of Bacteroides and lower Firmicutes were detected using 515f/806r compared to 27f/1492r and 27f*/1495f primers. So, the question is whether a gold standard of Firmicutes/Bacteroidetes ratio is a valuable and reliable universal marker, since two primer sets towards 16S rRNA can provide opposite information. Moreover, significantly higher relative abundance of Proteobacteria was detected using 27f/1492r. The beta diversity of sample groups differed remarkably and so the number of observed bacterial genera.

Striking antitumor activity of a methinium system with incorporated quinoxaline unit obtained by spontaneous cyclization.

A novel pentamethinium salt was synthesized with an unforeseen expanded conjugated quinoxaline unit directly incorporated into a pentamethinium chain. The compound exhibited high fluorescence intensity, selective mitochondrial localization, high cytotoxicity, and selectivity toward malignant cell lines, and resulted in remarkable in vivo suppression of tumor growth in mice.

16S rRNA gene mutations associated with decreased susceptibility to tetracycline in Mycoplasma bovis.

Mycoplasma bovis isolates with decreased susceptibilities to tetracyclines are increasingly reported worldwide. The acquired molecular mechanisms associated with this phenomenon were investigated in 70 clinical isolates of M. bovis. Sequence analysis of the two 16S rRNA-encoding genes (rrs3 and rrs4 alleles) containing the primary binding pocket for tetracycline (Tet-1 site) was performed on isolates with tetracycline hydrochloride MICs of 0.125 to 16 µg/ml. Mutations at positions A965T, A967T/C (Escherichia coli numbering) of helix 31, U1199C of helix 34, and G1058A/C were identified. Decreased susceptibilities to tetracycline (MICs, ≥2 µg/ml) were associated with mutations present at two (A965 and A967) or three positions (A965, A967, and G1058) of the two rrs alleles. No tet(M), tet(O), or tet(L) determinants were found in the genome of any of the 70 M. bovis isolates. The data presented correlate (P<0.0001) the mutations identified in the Tet-1 site of clinical isolates of M. bovis with decreased susceptibility to tetracycline.

Hepatoerythropoietic Porphyria Caused by a Novel Homoallelic Mutation in Uroporphyrinogen Decarboxylase Gene in Egyptian Patients.

Porphyrias are metabolic disorders resulting from mutations in haem biosynthetic pathway genes. Hepatoerythropoietic porphyria (HEP) is a rare type of porphyria caused by the deficiency of the fifth enzyme (uroporphyrinogen decarboxylase, UROD) in this pathway. The defect in the enzymatic activity is due to biallelic mutations in the UROD gene. Currently, 109 UROD mutations are known. The human disease has an early onset, manifesting in infancy or early childhood with red urine, skin photosensitivity in sun-exposed areas, and hypertrichosis. Similar defects and links to photosensitivity and hepatopathy exist in several animal models, including zebrafish and mice. In the present study, we report a new mutation in the UROD gene in Egyptian patients with HEP. We show that the homozygous c.T163A missense mutation leads to a substitution of a conserved phenylalanine (amino acid 55) for isoleucine in the enzyme active site, causing a dramatic decrease in the enzyme activity (19 % of activity of wild-type enzyme). Inspection of the UROD crystal structure shows that Phe-55 contacts the substrate and is located in the loop that connects helices 2 and 3. Phe-55 is strictly conserved in both prokaryotic and eukaryotic UROD. The F55I substitution likely interferes with the enzyme-substrate interaction.

Molecular characterization of acquired enrofloxacin resistance in Mycoplasma synoviae field isolates.

The in vitro activity of enrofloxacin against 73 Mycoplasma synoviae field strains isolated in Israel and Europe was determined by broth microdilution. Decreased susceptibility to enrofloxacin was identified in 59% of strains, with the MICs ranging from 1 to >16 µg/ml. The estimated MIC50 and MIC90 values for enrofloxacin were 2 and 8 µg/ml, respectively. Moreover, this study showed that 92% of recent Israeli field isolates (2009 to 2011) of M. synoviae have MICs of ≥ 2 µg/ml to enrofloxacin. Comparison of the quinolone resistance-determining regions (QRDRs) in M. synoviae isolates revealed a clear correlation between the presence of one of the amino acid substitutions Asp79-Asn, Thr80-Ala/Ile, Ser81-Pro, and Asp84-Asn/Tyr/His of the ParC QRDR and decreased susceptibility to enrofloxacin (MIC, ≥ 1 µg/ml). Amino acid substitutions at positions GyrA 87, GyrB 401/402, and ParE 420/454 were also identified, but there was no clear-cut correlation with susceptibility to enrofloxacin. Comparison of vlhA molecular profiles revealed the presence of 9 different genotypes in the Israeli M. synoviae field isolates and 10 genotypes in the European isolates; only one vlhA genotype (type 4) was identified in both cohorts. Based on results of vlhA molecular typing, several mechanisms for emergence and dissemination of Israeli enrofloxacin-resistant M. synoviae isolates are suggested.

Discrepancy between minimal inhibitory concentration to enrofloxacin and mutations present in the quinolone-resistance determining regions of Mycoplasma gallisepticum field strains.

Molecular characterization of the quinolone-resistance determining regions (QRDRs) of DNA gyrase and topoisomerase IV in 93 Mycoplasma gallisepticum field strains isolated in different geographic regions revealed discrepancies between minimal inhibitory concentration values and presence of amino acid substitutions within the QRDRs of GyrA and ParC in 9/93 (10%) strains. This may delimitate applicability of a gene-based assay to detect fluoroquinolone resistance in this avian pathogen.

Toll-like receptors in immune response to the viral infections.

Toll-like receptors (TLRs) are members of the innate immunity system. They are responsible for the recognition of various antigens and take part in the modulation of immunity responses. In general, they are divided into "bacterial" and "viral" TLRs, even though this classification overlaps in some cases. Genetic similarity of TLRs gives them the status of highly conservative proteins throughout the animal kingdom. However, there is a certain level of variation between different species that can result in semi-disparate recognition ability. Furthermore, their universal signaling pathways predispose them not only as a target for vaccination trials in humans, but also for the genetic selection in veterinary medicine. Moreover, the selection pressure and their conservative properties make them a suitable system for the evolutionary studies, since each separate genetic system has its own unique ortholog/paralog. TLRs 2, 3, 4, 7, 8, and 9 play a crucial role in the recognition and modulation of the innate immunity in response to the viral infection due to their predominant localization on the white blood cells and endothelial cells, while intracellularly localized TLRs lead the way.

Development and evaluation of a novel single-nucleotide-polymorphism real-time PCR assay for rapid detection of fluoroquinolone-resistant Mycoplasma bovis.

Monitoring of the susceptibility of Mycoplasma bovis field isolates to antibiotics is important for the appropriate choice of treatment. However, in vitro susceptibility testing of mycoplasmas is technically demanding and time-consuming, especially for clinical isolates, and is rarely performed in mycoplasma diagnostic laboratories. Thus, the development of methods allowing rapid real-time detection of resistant strains of M. bovis in clinical samples is a high priority for successful treatment. In this study, a novel TaqMan single-nucleotide-polymorphism (SNP) real-time PCR assay, which enables the rapid identification of M. bovis strains with different susceptibilities to fluoroquinolones, was developed and evaluated. The TaqMan SNP real-time PCR assay is based on the amplification of a 97-bp fragment of the parC quinolone resistance-determining region (QRDR) and allows the specific detection of four possible genotypes: GAC or GAT (susceptible to fluoroquinolones) and AAC or AAT (resistant to fluoroquinolones). Four TaqMan minor groove binder (MGB) probes identifying 1-base mismatches were designed and applied in a dual-probe assay with two reaction tubes. The TaqMan SNP real-time PCRs developed are highly specific for M. bovis, with a detection limit of 5 fg/microl (about 5 M. bovis genomes). In addition, all four SNP real-time PCR tests have almost the same efficiency (97.7% [GAC], 94% [AAC], 99.99% [GAT], and 98% [AAT]). Taken together, the data suggest that this SNP real-time PCR assay has potential as a routine diagnostic test for the detection of decreased susceptibility of M. bovis to fluoroquinolones.

Rapid detection of a point mutation in the parC gene associated with decreased susceptibility to fluoroquinolones in Mycoplasma bovis.

Comparison of the quinolone resistance-determining regions (QRDRs) in 42 Mycoplasma bovis clinical isolates revealed amino acid substitutions at both GyrA (position 83) and ParC (position 84) in 10/11 enrofloxacin-resistant strains. The mutation present in the parC QRDR was discriminative for enrofloxacin resistance by parC PCR-restriction fragment length polymorphism. Comparison of molecular profiles by insertion sequence typing suggests that the currently prevalent enrofloxacin-resistant M. bovis strain evolved by selection under field conditions from one of the susceptible strains.

Perception of stroke in Croatia--knowledge of stroke signs and risk factors amongst neurological outpatients.

BACKGROUND AND PURPOSE: The aim of this hospital-based survey was to determine baseline stroke knowledge in Croatian population attending the outpatient services at the Department of Neurology. METHODS: A multiple choice questionnaire was designed, divided into three sections: (i) demographic data, (ii) knowledge of stroke risk factors and stroke signs and (iii) actions the patients would undertake if confronted with risk of stroke and information resources regarding health. RESULTS: The analysis included 720 respondents (54.9% women). The respondents most frequently indicated stroke symptoms as following: speech disorder 82%, paresthesiae on one side of the body 71%, weakness of arm or leg 55%, unsteady gait 55%, malaise 53%, monocular loss of vision 44%. The risk factors most frequently identified were hypertension 64%, stress 61%, smoking 59%, elevated lipids 53%, obesity 52%, coagulation disorder 47%, alcoholism 45%, low-physical activity 42%, elderly age 39%, cardiac diseases 38%, weather changes 34%, drugs 33% and diabetes 32%. If confronted with stroke signs 37% of respondents would consult the general practitioner and 31% would call 911 or go to a neurologist. Amongst patients with a risk factor, only diabetics were aware that their risk factor might cause stroke (P < 0.001). Respondents with lowest education had the least knowledge regarding stroke signs (P < 0.01). DISCUSSION: The results of this study indicate that respondents showed a fair knowledge about stroke signs and risk factors for stroke. The results of our study will help to create and plan programmes for improvement of public health in Croatia.

Toll-like receptors TLR1, TLR2 and TLR4 gene mutations and natural resistance to Mycobacterium avium subsp. paratuberculosis infection in cattle.

Toll like receptors (TLRs) are a class of pattern recognition receptors belonging to the innate immune system. Mutations in the protein coding region of TLRs are associated with altered responsiveness to pathogen-associated molecular patterns (PAMPs). A search was performed for novel mutations in bovine TLR1, TLR2 and TLR4 genes associated with the Mycobacterium avium subsp. paratuberculosis (MAP) infection. The work was also focused on the assessment of linkage between well known mutations in TLR genes (TLR2: Arg677Trp, Pro681His and Arg753Gln; TLR4: Asp299Gly and Thr399Ile), and the susceptibility of cattle to MAP infection. Detection of MAP infection in cattle population (n=711) was based on IS900 PCR, which revealed 22.50% (n=160) MAP positivity. Known mutations in TLR2 and TLR4 genes were not found in cattle population. A novel mutation Val220Met was associated (Odd's ratio, OR-3.459) with increased susceptibility to MAP infection. Toll/interleukin-1 receptor (TIR) domain of TLR2 was screened for the presence of mutations, wherein a novel Ile680Val mutation was linked with MAP infection. In silico analysis of the bovine TLR4 ectodomain (ECD) revealed the polymorphic nature of the central ECD and irregularities in the central LRR motifs. LRR11 of the TLR4 showed five missense mutations possibly linked with the increased susceptibility to MAP infection. The most critical position that may alter the pathogen recognition of TLR molecule was 4th residue downstream to LRR domain. Two such missense mutations in TLR4 (Asp299Asn downstream to LRR11, and Gly389Ser downstream to LRR15) were associated with MAP infection. Briefly, the work describes novel mutations in the bovine TLRs and presents their association with the MAP infection.

[Use of Streptococcus agalactiae sak0192 gene polymorphism as a molecular epidemiologic marker].

AIM: To study structure of sak0192 gene in S. agalactiae strains isolated from animals and to assess potential for using it as a molecular epidemiologic marker. MATERIALS AND METHODS: One hundred and fourteen strains of S. agalactiae isolated from cow milk were used. Presence of sak0192 gene as well as pathogenicity genes bac, bca, scpB was determined by PCR. Alleles of sak0192 gene were identified by SSCP method, and their nucleotide sequences--by sequencing. RESULTS: In sak0192 gene of S. agalactiae strains direct repeats and spacers were revealed as well as heterogeneity in its nucleotide sequence. Eight different alleles of sak0192 gene were identified in 114 strains, five of which were characteristic only for strains isolated from animals. Complex analysis of sak0192 gene allele and presence of bac, bca, and scpB revealed 16 different genetic variants, only 3 of which were characteristic for strains isolated from animals and from humans. CONCLUSION: Polymorphism of sak0192 gene could be used for diagnostics and differentiation of S. agalactiae strains and, together with combination of pathogenicity genes bac, bca, and scpB, for identification of epidemically significant clones--agents of infectious disease in humans and animals.

Pineal gland cyst evaluated by transcranial sonography.

Transcranial sonography (TCS) has never been used in the evaluation of morphology of pineal gland. The aim of the study was to assess the possibility of TCS to distinguish normal from cystic pineal gland and to correlate its size with magnetic resonance imaging (MRI) at the first examination and during follow-up. Sixty patients with previously made MRI of the brain were evaluated by two independent observers using TCS, blinded to the results of the MRI. Inappropriate bone window limited TCS examination in seven patients. All 14 pineal gland cysts (PGC) seen on MRI were detected by both observers using TCS. Control group consisted of 39 healthy examinees. No statistically significant difference has been found between: PGC size measured by first and second observer by TCS (P = 0.425), PGC size measured by TCS and MRI (first observer, P = 0.353; second observer, P = 0.425), size of the pineal gland measured by TCS and MRI in control group (first observer, P = 0.497; second observer, P = 0.370) or interobserver variability in control group (P = 0.373). The MRI and TCS follow-up of ten patients after six months did not show any difference in size of PGC. TCS can be used as a method in detection, measurement and follow-up of PGC.

PrP gene polymorphism in sheep breeds in Slovakia and susceptibility to scrapie.

We analyzed the prion protein (PrP) genotype based on the codons 136, 154 and 171 and assigned to five risk groups (R1-R5) in healthy and scrapie-affected sheep in Slovakia. In healthy (asymptomatic) population, 119 Merino, 106 Improved Valachian, 117 Tsigai, and 48 Suffolk breeds were tested. Among the asymptomatic sheep, the low-risk genotypes R1 and R2 were most abundant in Suffolk (94%) and Merino (84%) breeds, followed by Tsigai (58%) and Improved Valachian (40%) breeds. The medium-risk group R3 was most frequent in Improved Valachian (31%) breed, followed by Tsigai (21%), Merino (10%), and Suffolk (6%) breeds. The occurrence of high-risk groups R4 and R5 was none in Suffolk breed, followed by Merino (6%), Tsigai (21%), and Improved Valachian (30%) breeds. Since 2003, altogether 48 cases of scrapie have been confirmed in Tsigai (38), Merino (4), Improved Valachian (2), Improved Valachian x Tsigai (3), and Suffolk (1) breeds. Among sheep with scrapie, Merino breed belonged to the medium-risk group R3. The majority of scrapie-affected Tsigai sheep were classified into high-risk R5 (50%) and medium-risk R3 (42%) groups. We showed an association of scrapie with medium- and high-risk groups of PrP genotype in Slovakia. In particular, the glutamine at position 171 appears to be of major importance for the susceptibility to scrapie.

Toll-like receptor gene polymorphism and its relationship with somatic cell concentration and natural bacterial infections of the mammary gland in sheep.

Possible correlation between Toll-like receptor (TLR)-gene mutations and the susceptibility of the mammary gland to bacterial infections and also the associate breed-dependent aspects of somatic cell concentration (SCC), bacterial infection and TLR-gene mutations in sheep are described. In Polish Lowland Sheep (PLS), milk samples exceeding the level of 500/microL (i.e. 5 x 10(5) per mL) of SCC were recorded almost twice more frequently than in Polish Heath Sheep (PHS) (40 and 22.3%, respectively). The frequency of bacterial infections was also found in a similar ratio (20 and 12.7%, respectively). During detection of the TLR-gene mutation we recorded 2 alleles of TLR1, 6 alleles of TLR2 and 10 alleles of TLR4 genes in PHS sheep, while PLS sheep possessed 2, 4 and 6 alleles, respectively. Statistical analyses revealed a relationship between the specified TLR alleles, SCC and the frequency of incidence of bacterial inflammations of mammary gland. The data may serve as a benchmark for further study of TLR-gene mutation-dependent predisposition of mammary gland defensive cells to recognize the pathogen properly and initiate the immunological response, and may help in identifying one of the markers of natural resistance against sheep mastitis.

Molecular epidemiology of group B streptococcal infections.

Streptococcus agalactiae (GBS) is a causative agent of sepsis and meningitis in newborns and diseases in pregnant women and nonpregnant adults. Various approaches, including both nongenetic and genetic techniques, are currently used for the study of epidemiology of GBS infections. In the present paper the different methods of molecular epidemiology of GBS infections are reviewed, and several novel approaches are introduced. The advantages and disadvantages of molecular methods are discussed and compared with traditional serotyping technique. The possible use of the molecular approaches for identification of different genetic lineages in GBS as well as for identification and control of the epidemiologically actual clones is discussed.

Characterization of a complex restriction-modification system detected in Staphylococcus aureus and Streptococcus agalactiae strains isolated from infections of domestic animals.

Characterization of classic type II restriction-modification systems (RMS) (restriction endonucleases and modification methyltransferases) was carried out in isolates of Staphylococcus aureus and Streptococcus agalactiae obtained from clinical material. Among the 100 isolates of S. aureus two different RMS type II were detected. The first was expressed in isolates 32 and 33 (Sau32 I and Sau33 I); the targeting sequence was determined as 5'-GGN CC-3' (Sau96 I isoschizomer). The second was found in isolates no. 90, 93, 96*, and 98 (Sau90 I, Sau93 I, Sau96* I, Sau98 I) and enzymes recognized sequence 5'-CTY RAG-3' (SmlI isoschizomer). Analysis of 40 isolates of S. agalactiae revealed only one RMS; it was detected in two isolates (no. 16 and 23; Sag16 I and Sag23 I). Restriction endonuclease expressed by these isolates cleaved DNA in sequence 5'-CTG CA/G-3' (PstI isoschizomer). In RMS-positive S. aureus and S. agalactiae isolates plasmid DNA capable of replication in Escherichia coli and Bacillus subtilis was also detected and isolated.

Presence of insertion sequences (IS elements) in group B streptococci of bovine origin.

BACKGROUND & OBJECTIVES: Streptococcus agalactiae (group B streptococci, GBS) is one of the leading causative agents of human and animal infections. Recently it was demonstrated that integration of different IS elements could inactivate some of the GBS virulence properties. The presence of IS elements in human isolates has been studied while the bovine isolates were not investigated till now. The objective of the study was to perform IS analysis of a large number of bovine GBS and to use the IS elements for classification and molecular epidemiology of GBS strains. METHODS: A total of 101 GBS isolates obtained from the dairy cows were tested. These were analyzed by PCR and multiplex PCR. Southern hybridization was accomplished with the Enzo(TM) DNA Labeling and Detection Kit. The computer techniques were used for selection of the specific primers and for analysis of the sizes of PCR products. RESULTS: GBS isolates collected at three different dairy farms were studied for the presence of IS elements. Multiplex PCR was used for the fast screening. It was found that IS861 presented in 29 GBS isolates (28.7%), IS1548 in 9 (8.9%), ISSa4 in 48 (47.5%) and IS1381 in 26 isolates (25.7%). A total of 28 bovine GBS isolates (27.7%) did not possess any of the IS elements, 36 (35.6%) possessed, 35 (34.7%) possessed two and 2 (1.9%) possessed three different IS elements. The GBS with four different IS elements were not found. Taken together, 10 different variants of GBS strains were discovered. Two out of 10 variants being specific for 51 isolates (50.5%) were predominant in bovine GBS. The results of the study demonstrated that the presence of IS elements significantly varied in bovine GBS. INTERPRETATION & CONCLUSION: The present data demonstrated that variants of IS elements present in GBS genome could be used as effective criteria for molecular epidemiology. In future this approach could probably be used as an additional tool for the epidemiological control and prevention of other bacterial infections.

Elaboration of enzyme immunoassay based on recombinant antigens and intended for diagnostics of syphilis.

Enzyme immunoassay (EIA) using recombinant antigens for the detection of Treponema pallidum-specific antibodies in sera of syphilis patients was developed. Four low-molar-mass Treponema antigens (Tp15, Tp17, TmpA, Tp47) were investigated; 17- and 47-kDa proteins were demonstrated as immunodominant as they permitted to obtain the most sensitive EIA. Using a mixture of these proteins a 3rd-generation-EIA kit Dia-Syph was constructed, its sensitivity being 99.4% during tests of 165 sera of syphilitic patients. No false result was obtained on the commercial panel PSS01 (BBI, USA). The specificity of the elaborated test system (99.7%) was determined on 295 sera.

The PrP genotype of sheep of the improved Valachian breed.

In a worldwide majority of sheep breeds an excessive susceptibility to scrapie associated with the PrP gene alleles coding for valine (V; at the 136 codon) and glutamine (Q; at the 171 codon) (e.g., VRQ/VRQ, VRQ/ARQ, or ARQ/ARQ) was demonstrated. Particularly the PrPVRQ allele is closely associated with the high-risk development of the disease; the PrPARQ allele can also fulfill this function but under certain limited conditions. Polymorphism in the PrP gene sequences (conclusively related to the increased susceptibility of sheep to scrapie) of improved Valachian sheep from two Slovak regions, Orava and Spis, was determined. Examination of 735 sheep showed that ARR/ARQ was the most frequent genotype (45.2%). High-risk genotypes were determined in 32.4% of sheep (ARQ/ARQ 19.3, ARR/VRQ 9.0, ARR/VRQ 3.5, VRQ/VRQ 0.3, ARR/VRR 0.3). Low-risk genotypes were found in 67.7% of sheep (ARR/ARQ 45.2, ARR/ARR 10.9, ARR/AHQ 5.7, ARQ/ARQ 4.9, AHQ/AHQ 0.7, ARR/AHR 0.3). Despite the geographically distant flocks of improved Valachian sheep investigated no difference in the occurrence of individual PrP genotypes was observed.