The species Acinetobacter calcoaceticus, A. baumannii, genomic species 3, and genomic species 13TU included in the Acinetobacter calcoaceticus-Acinetobacter baumannii complex are genetically highly ...related and difficult to distinguish phenotypically. Except for A. calcoaceticus, they are all important nosocomial species. In the present study, the usefulness of the 16S-23S rRNA gene intergenic spacer (ITS) sequence for the differentiation of (genomic) species in the A. calcoaceticus-A. baumannii complex was evaluated. The ITSs of 11 reference strains of the complex and 17 strains of other (genomic) species of Acinetobacter were sequenced. The ITS lengths (607 to 638 bp) and sequences were highly conserved for strains within the A. calcoaceticus-A. baumannii complex. Intraspecies ITS sequence similarities ranged from 0.99 to 1.0, whereas interspecies similarities varied from 0.86 to 0.92. By using these criteria, 79 clinical isolates identified as A. calcoaceticus (18 isolates) or A. baumannii (61 isolates) with the API 20 NE system (bioMérieux Vitek, Marcy l'Etoile, France) were identified as A. baumannii (46 isolates), genomic species 3 (19 isolates), and genomic species 13TU (11 isolates) by ITS sequencing. An identification rate of 96.2% (76 of 79 isolates) was obtained by using ITS sequence analysis for identification of isolates in the A. calcoaceticus-A. baumannii complex, and the accuracy of the method was confirmed for a subset of strains by amplified rRNA gene restriction analysis and genomic DNA analysis by AFLP analysis by using libraries of profiles of reference strains. In conclusion, ITS sequence-based identification is reliable and provides a promising tool for elucidation of the clinical significance of the different species of the A. calcoaceticus-A. baumannii complex.
Infections caused by yeasts have increased in previous decades due primarily to the increasing population of immunocompromised patients. In addition, infections caused by less common species such as ...Pichia, Rhodotorula, Trichosporon, and Saccharomyces spp. have been widely reported. This study extensively evaluated the feasibility of sequence analysis of the rRNA gene internal transcribed spacer (ITS) regions for the identification of yeasts of clinical relevance. Both the ITS1 and ITS2 regions of 373 strains (86 species), including 299 reference strains and 74 clinical isolates, were amplified by PCR and sequenced. The sequences were compared to reference data available at the GenBank database by using BLAST (basic local alignment search tool) to determine if species identification was possible by ITS sequencing. Since the GenBank database currently lacks ITS sequence entries for some yeasts, the ITS sequences of type (or reference) strains of 15 species were submitted to GenBank to facilitate identification of these species. Strains producing discrepant identifications between the conventional methods and ITS sequence analysis were further analyzed by sequencing of the D1-D2 domain of the large-subunit rRNA gene for species clarification. The rates of correct identification by ITS1 and ITS2 sequence analysis were 96.8% (361/373) and 99.7% (372/373), respectively. Of the 373 strains tested, only 1 strain (Rhodotorula glutinis BCRC 20576) could not be identified by ITS2 sequence analysis. In conclusion, identification of medically important yeasts by ITS sequencing, especially using the ITS2 region, is reliable and can be used as an accurate alternative to conventional identification methods.
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (Bruker Biotyper) was able to accurately identify 98.6% (142/144) of Acinetobacter baumannii isolates, ...72.4% (63/87) of A. nosocomialis isolates, and 97.6% (41/42) of A. pittii isolates. All Acinetobacter junii, A. ursingii, A. johnsonii, and A. radioresistens isolates (n = 28) could also be identified correctly by Bruker Biotyper.
Biodegradation of petroleum hydrocarbon oil (14,000 mg kg
−1) were investigated in six biopiles batches, differing in the remediation strategy: bioaugmentation (selected consortium and kitchen waste ...were introduced), biostimulation (added with rhamnolipid, high-level, or low-level nutrient), and bioaugmentation plus biostimulation (added both with rhamnolipid and bacterial consortia). After the 140-day operation, the kitchen waste (KW) and the low-level nutrient (NEL) batches achieved the highest total petroleum hydrocarbon degradation efficiency (>80%). The result of the hydrocarbon analysis revealed that the bioaugmentation approaches were the most effective ones in removing aromatic component (64% and 68%), and KW and NEL were the only two approaches that can remove the polar component with positive efficiency, 11% and 21%, respectively. The terminal-restriction fragment length polymorphism percentage (T-RFLP) abundance applied with nonmetric multidimensional scaling indicated a similarity of the bacterial communities during the early fastest remediation stage. The results of the oligonucleotide array targeting the ribosomal internal transcribed spacer (ITS) region, along with the hydrocarbon fractional analysis, indicated a successive degradation completed by the bacterial–fungi consortia. Before Day 70, the bacterial community was dominant in decomposing the saturated and partially aromatic hydrocarbons. After Day 70, the fungal community found to be dynamic and responsible for degradation of the polar hydrocarbons composing of recalcitrant metabolites.
► Kitchen waste and low-level nutrient enhancement were the most efficient remediation means. ► T-RFLP data in MDS indicated similarity of bacterial communities in the 1st remediation stage. ► ITS and hydrocarbon fraction data proved a successive degradation pattern by bacteria and fungi. ►
Aspergillus fumigatus and
Fusarium oxysporum were useful in degrading recalcitrant compounds.
Although it has been known for decades that patients with type 2 diabetes mellitus (DM) are more susceptible to severe tuberculosis (TB) infection, the underlying immunological mechanisms remain ...unclear. Resistin, a protein produced by immune cells in humans, causes insulin resistance and has been implicated in inhibiting reactive oxygen species (ROS) production in leukocytes. Recent studies suggested that IL-1β production in patients with Mycobacteria tuberculosis infection correlates with inflammasome activation which may be regulated by ROS production in the immune cells. By investigating the level of resistin in different patient groups, we found that serum resistin levels were significantly higher in severe TB and DM-only groups when compared with mild TB cases and healthy controls. Moreover, elevation of serum resistin correlated with impairment of ROS production of neutrophils in patients with both DM and TB. In human macrophages, exogenous resistin inhibits the production of ROS which are important in the mycobacterium-induced inflammasome activation. Moreover, macrophages with defective ROS production had poor IL-1β production and ineffective control of mycobacteria growth. Our results suggest that increased resistin in severe TB and DM patients may suppress the mycobacterium-induced inflammasome activation through inhibiting ROS production by leukocytes.
The incidence of yeast infections has increased in the recent decades, with Candida albicans still being the most common cause of infections. However, infections caused by less common yeasts have ...been widely reported in recent years. Based on the internal transcribed spacer 1 (ITS 1) and ITS 2 sequences of the rRNA genes, an oligonucleotide array was developed to identify 77 species of clinically relevant yeasts belonging to 16 genera. The ITS regions were amplified by PCR with a pair of fungus-specific primers, followed by hybridization of the digoxigenin-labeled PCR product to a panel of oligonucleotide probes immobilized on a nylon membrane for species identification. A collection of 452 yeast strains (419 target and 33 nontarget strains) was tested, and a sensitivity of 100% and a specificity of 97% were obtained by the array. The detection limit of the array was 10 pg of yeast genomic DNA per assay. In conclusion, yeast identification by the present method is highly reliable and can be used as an alternative to the conventional identification methods. The whole procedure can be finished within 24 h, starting from isolated colonies.
The performance of the BluePoint MycoID plus kit (Bio Concept Corporation, Taichung, Taiwan), which was designed to simultaneously detect Mycobacterium tuberculosis (MTB), rifampin- and ...isoniazid-resistant MTB, and nontuberculous mycobacteria (NTM) was first evaluated with 950 consecutive positive cultures in Mycobacterium Growth Indicator Tube (MGIT) system (BACTEC, MGIT 960 system, Becton-Dickinson, Sparks) from clinical respiratory specimens. The discrepant results between kit and culture-based identification were finally assessed by 16S rRNA gene sequencing and clinical diagnosis. The accuracy rate of this kit for identification of all Mycobacterium species was 96.3% (905/940). For MTB identification, the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the kit were 99.7%, 99.3%, 99.0% and 99.8%, respectively. For rifampicin-resistant MTB identification, the sensitivity, specificity, PPV, and NPV of the kit were 100.0%, 99.4%, 91.3%, and 100.0%, respectively, while the corresponding values of isoniazid-resistant MTB identification were 82.6%, 99.4%, 95.0%, and 97.6%, respectively. In identifying specific NTM species, the kit correctly identified 99.3% of M. abscessus (147/148) complex, 100% of M. fortuitum (32/32), M. gordonae (38/38), M. avium (39/39), M. intracellulare (90/90), M. kansasii (36/36), and M. avium complex species other than M. avium and M. intracellulare (94/94). In conclusions, the diagnostic value of the BluePoint MycoID plus kit was superior to culture method for recoveries and identification of NTM to species level. In addition, the diagnostic accuracy of BluePoint MycoID plus kit in MTB identification was similar to conventional culture method with high accuracy rate of rifampicin-resistant M. tuberculosis identification.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Bioremediation of diesel-contaminated soils were applied to investigating effects of soil organic matter (SOM) and bacterial community shift. Soil samples were artificially contaminated with diesel ...oil, ranging from 4000 to 12000 mg/kg soil, remediated with laboratory-scale landfarming batch applications. The SOM levels in our experiment were 2.3% (presented as SOM15), 8.9% (SOM092), and 11.8% (SOM125). Based on each of the SOM levels, bioremediation approaches of bioaugmentation (BA015, BA092, and BA125) and using indigenous microorganisms as control groups (CT015, CT092, and CT125) were tested. After about 300-day operation, total petroleum hydrocarbon (TPH) degradation efficiency became 73%, 63%, and 59% in SOM015, SOM092, and SOM125, respectively. Their 1st order degradation rates also reduced with the increase of SOM. We preliminarily concluded that SOM affected the TPH degradation efficiency and 1st degradation rates. With a logarithm transformation, the degradation pattern of SOM092 and SOM125 found to resemble each other. No apparent improvement was found from the BA batches. Our Intergenic spacer (ITS) microarray result indicated the existence of diesel-degrading bacteria in the indigenous communities. Nonmetric multidimensional scaling (MDS) based on terminal restriction fragment length polymorphism (T-RFLP) data indicated that 1) CT community became similar to BA community, once the 1st degradation stage started, impling an activation of the indigenous bacteria; 2) the degradation stage affected the community dynamics more than the SOM or the remediation approaches could do, and 3) both BA092 and BA125 located in the same cluster on the MDS plot all the time, revealing the similar communities. The similar communities might cause the comparable degradation patterns in SOM092 and SOM125. The bacteria community shift found useful in explaining the TPH degradation performance.
► The total petroleum hydrocarbon degradability reduced with the increase of soil organic matter. ► The Intergenic spacer array identified diesel degrading bacteria in the indigenous community. ► The ITS array explained the similar TPH degradability between the control and experimental tests. ► The MDS plot based on T-RFLP revealed the degradation stages affected the community dynamics most.
Cryptococcus albidus keratitis is a rare and difficult diagnosed disease. Here we report a case of C albidus keratitis early diagnosed by dot hybridization assay and successfully treated with ...intrastromal injection of Amphotericin B (AB).A 45-year-old man presented with left red eye for 2 days. The slit lamp examination exhibited deep corneal infiltrations. Smears and cultures were performed but revealed negative findings. Molecular detection of pathogens was performed by dot hybridization assay, and C albidus keratitis was diagnosed. Despite the identification of C albidus, the clinical condition still worsened due to deep corneal infiltration. After performing intrastromal injection of AB, the corneal infiltration gradually improved.C albidus is a rare cause of diseases in humans and should be considered as a potential pathogen of corneal ulcer. The prognosis of C albidus keratitis will improve if the condition is recognized early and treated properly.
Staphylococcus aureus (S. aureus) is one of the most common pathogens that causes infectious and foodborne diseases worldwide. Searching for drug and chemical compounds against this bacterium is ...still in demand. We found that grape seed extract (GSE), a natural food product rich in polyphenols, inhibited the dihydrofolate reductase activity and growth of
S. aureus. In addition, the intracellular content of tetrahydrofolate (THF), the major folate species identified in
S. aureus, was significantly decreased when GSE was present in medium. The GSE-induced growth inhibition was reversed by adding, THF, 5,10-methylenetetrahydrofolate or methionine to the medium. The differential rescuing effects elicited by thymidine and methionine indicated that GSE-induced perturbation in folate-mediated one-carbon metabolism has more profound impact on methionine cycle than on thymidine monophosphate (TMP) synthesis. Significantly reduced inflammatory responses and mortality were observed in zebrafish infected with
S. aureus pre-incubated with GSE. We conclude that GSE might serve as an effective natural alternative for the control of food poisoning caused by
S. aureus with proper safety measure.
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