Rapid detection and identification of fungi in urine samples by pyrosequencing / 中华传染病杂志

Objective To establish a rapid method for the clinical detection and identification of fungi in clinical urine samples.Methods DNA was extracted from clinically collected urine sample,and the fungal ribosomal internal transcribed spacer was amplified by polymerase chain reaction (PCR) and followed by pyrosequencing.The fungal species were identified by sequence alignment.Results The identification results were compared between PCR-pyrosequencing and conventional culture method.Among the 1320 urine samples,180 were detected positive by conventional method with the positive rate of 13.6％,while 192 were positive by the pyrosequencing based method with the positive rate of 14.5％.The overall coincidence rate of the two methods was 99.09 ％,with the positive coincidence rate of 100 ％ and the negative coincidence rate of 98.95 ％.The Kappa value was 0.963,suggesting a good consistency.The results of 13 standard strains were consistent with the actual results.Conclusions A rapid culturefree method for the detection of fungi in urine sample has been successfully established.This method is based on PCR-pyrosequencing technology with highly accuracy,sensitivity and reproducibility.It is highly automated,cost effective and with high throughput (96 samples per run).The fungal pathogen in urine is identified by single step test within 3 hours without conventional culture.Thus,it is applicable in the clinical laboratory.

Application of Specific Fragment Length Polymorphism of Algae rDNA in Identification of Drowning Cases / 法医学杂志

OBJECTIVES@#To identify the drop-off location of victims in drowning cases, and confirm whether it is a fatal drowning or the victim is thrown into the water after death by detecting part of 5.8S sequence and second internal transcribed spacer （ITS2） （5.8S+ITS2） of diatom rDNA in water and organs.@*METHODS@#Two cases identified by diatom examination, which received by Nanjing Municipal Public Security Bureau Forensic Center, were taken as the research objects. The difference of the population structure of algae in water and human tissue was analysed by length polymorphism of 5.8S+ITS2 marker.@*RESULTS@#In case 1, similar species of diatom were detected from victim's lung and liver tissues and the water sample. Two kinds of DNA fragments with length of 330 bp and 376 bp were detected from victim's lung tissue and the water sample using 5.8S+ITS2 marker, which could confirm the victim was drowning before death. In case 2, there was no diatom found in victim's lung and liver tissues. Only one kind of DNA fragment with length of 331 bp and low relative fluorescence unit （RFU） was obtained from victim's lung tissue using 5.8S+ITS2 marker, thus the victim was thrown into the water after death.@*CONCLUSIONS@#The experimental results of the two cases in present study are consistent with the actual facts and the result of the diatom microscopic examination. The difference of population structure of specific microorganism in water and human tissue can be detected by 5.8S+ITS2 marker, which can help to identify the drop-off location of victims in drowning cases, and confirm whether it is a fatal drowning or the victim is thrown into the water after death.

Impact of postnatal exposure to antibiotics on intestinal microbiome in preterm infants / 中华围产医学杂志

Objective To assess the impact of postnatal exposure to antibiotics on intestinal microbiome in preterm infants with 16S rDNA sequencing technology.Methods This study was conducted on 19 preterm infants admitted to the neonatal intensive care unit (NICU) at Tongji Hospital immediately after birth from September 2015 to February 2016.Two groups were set up according to the duration of antibiotic exposure (＜3 d,n=10;＞7 d,n=9).Fecal samples were collected from each infant within the first day and 2 or 3 weeks after bitrth.High-throughput sequencer (Hiseq 2500) was used for sequencing,from which information on composition and abundance of species,phylogenetic evolution and bacterial community diversity was obtained.Intergroup differences was analyzed with independent samples t-test or Fisher's exact test.Results (1) No statistically significant difference was found in general information about the infants between the two groups.(2) The intestinal flora in preterm infants was mainly composed of Lactococcus,Enterococcus and Bacillus for both groups before antibiotic treatment (36.41％,23.40％ and 14.98％).The proportions of Lactococcus and Bacillus were decreased significantly (1.73％ and 1.25％,P＜0.01) with Enterococcus becoming the predomiant genus (16.73％) after antibiotic treatment,while the relative proportions of Staphylococcus,Clostridium and Bifidobacterium were raised.(3) The Shannon index was decreased after antibiotic exposure [(2.34±0.84) vs (1.06±0.96) in ＜3 d group,and (2.64± 1.04) vs (0.35±0.36) in ＞7 d group,both P＜0.05],and the other three Alpha diversity indexes,including observed species,Chaol and PD whole tree indexes,were also decreased within each group (all P＜0.05).(4) Bacterial assemblages showed high beta diversity in both groups before the usage of antibiotics,but antibiotic therapy reduced the diversity.(5) Anoism analysis showed significant differences in the composition of intestinal flora within each group before and after antibiotic exposure (R=0.555and 0.733,both P=0.001),but no difference was found between the two groups after antibiotic exposure (R=0.060,P=0.138).Conclusions Antibiotic exposure,even short-term (＜3 d) administration,may significantly change the distribution of intestinal microbiota in preterm infants.Prolonged usage of antibiotics could have detrimental influence on intestinal flora.Therefore,for preterm babies,prescription of antibiotics should be cautious,even short-term empirical usage.

Molecular identification of Trichophyton mentagrophytes complex strains in Hubei province / 中华皮肤科杂志

Objective To profile the intraspecific type of Trichophyton mentagrophytes clinically isolated from different anatomical sites of patients, and to compare the performance of different target sites for the identification of Trichophyton mentagrophytes complex strains. Methods A total of 48 Trichophyton mentagrophytes strains, which were clinically isolated from Department of Dermatology, Wuhan No. 1 Hospital in the latest 3 years, were included in this study. The phenotypes of these Trichophyton mentagrophytes isolates were primarily determined by morphological observation and the urease test. PCR was performed to amplify the nuclear ribosomal internal transcribed spacer(ITS) region and the D1?D2 domains of the large?subunit ribosomal DNA(28S rDNA)followed by DNA sequencing. Then, Clustal X2 software and MEGA 6.0 software were used to analyze the ITS and D1?D2 sequences and to build phylogenetic trees by the maximum?likelihood method (bootstrap = 2000). Results As the ITS sequence?based phylogenetic tree showed, the probability that the 48 isolates were grouped into the Trichophyton interdigitale clade reached 92%. However, Trichophyton interdigitale could not be effectively differentiated from Trichophyton quinckeanum by the D1?D2 sequence?based phylogenetic tree. In addition, Trichophyton interdigitale showed various appearances, including woolen type, downy type, cream type, powdery type and granular type. Conclusions Trichophyton mentagrophytes can be identified to the species level based on the sequence of ITS region, which shows higher efficiency in identifying Trichophyton mentagrophytes complex than the D1?D2 domains. Morphological characteristics can not serve as the basis for intraspecific typing of Trichophyton mentagrophytes.

The ability to identify the yeast-like fungi by YST identification cards and pyrosequencing analysis / 中华检验医学杂志

Objective To evaluate the ability of Vitek 2 Compact YST identification cards and pyrosequencing analysis for identifying the clinical isolates of yeast-like fungi.Methods Vitek 2 Compact YST identification cams and ITS1 region pyrosequencing analysis were used to identify the clinical isolates of yeast-like fungi at Jinan Military General Hospital in 2011.The strains which could not be identified to species by pyrosequencing analysis were identified again by the method of ITS1 region Sanger sequencing.The strains with inconsistent identified results by YST and pyrosequencing were identified again using API 20C.Results A total of 282 srtains were isolated from various clinical specimens for culturing in 2011.In addition to the three which could only be identified to similar species,other strains could be clearly identified to species by the method of ITS1 reverse pyrosequencing.Three strains which failed identified to species by pyrosequencing couldn't be distinguished fully by the method of Sanger sequencing.There were 7 strains unidentified,14 strains low discrimination(％ id ＜ 80％),and 6 strains misidentification using YST cams.The identification coincidence rate was 90.4％.The identification coincidence rates were various in different species of yeast-like fungi using YST cards.Conclusions The vast majority of clinical isolates of yeast-like fungi could be identified by ITS1 reverse pyrosequencing analysis.Vitek 2 Compact YST caRD basically meets the needs.But attention should be paid to the standard operating and regular internal quality control.For some rare species it is also needed to combine the source of specimen,colonies and characteristics to determine the identification results for the rare stains.

The clinical application of identification of Aspergillus spp.using ITS and β-tubulin gene sequences / 中华检验医学杂志

Objective To study the clinical application of the ITS and β-tubulin gene regions in identification of Aspergillus spp. Methods One hundred and twenty-four Aspergillus strains that isolated from fungal rhino-sinusitis specimens were collected in Beijing Tongren Hospital, Capital Medical University from July 2007 to January 2010. They were identified by morphological and molecular methods. The first one included traditional culture, slide culture, and microscopic examination after lactophenol cotton blue stain and KOH digestion. The second one was amplifying and sequencing the part of ITS and β-tubulin gene and aligned all the sequences in the GenBank, European Molecular Biology Laboratory nucleotide sequence database, and DNA Data Bank of Japan. Results Of the 56 Aspergillus flavus identified by morphological features, fifty-five isolates were identified as Aspergillus flavus and 1 isolates was Aspergillus parasiticus by the ITS and β-tubulin gene region sequence analysis. In the 37 Aspergillus fumigatus identified by morphological method, and all the 37 isolates were identified as species complex of Aspergillus fumigatus by the ITS region sequence analysis, but through the sequence analysis of β-tubulin gene region, thirty-five isolates were identified as Aspergillus. fumigatus and 2 were Aspergillus lentulus. Twenty-one isolates were identified as Aspergillus versicolor by morphological method, but 16 of them were identified as Aspergillus. versicolor and 5 can not be identified to species level by the ITS region sequence. And by comparative-sequence analysis of β-tubulin gene region, the 5 isolates were identified as Aspergillus sydowii,the other 16 isolates were Aspergillus. versilcolor. Ten isolates were identified as Aspergillus nidulans by morphological features, the ITS and β-tubulin gene region sequence analysis. Conclusions β-tubulin gene sequencing is more suitable for identifying Aspergillus, and could identify Aspergillus spp. to species level Sequences of ITS region could only identify Aspergillus spp. to species complex.

Primary exploration on identification of pathogenic Trichosporon spp. with rDNA-RFLP analysis / 中华皮肤科杂志

Objective To genotype Trichosporon spp. with rDNA-ITSAGSl-RFLP analysis followed by cluster analysis, and attempt to apply this method to rapid species identification of human pathogenic Trichosporon spp.. Methods Fourteen strains of Trichosporon, which belonged to 8 species, were collected. The rDNA-ITS/IGSl regions were amplified by PCR and sequenced. Simultaneously, the amplicons were digested separately with restriction enzymes, including Hae III, Hha I , Hae IH and Hha I , Hinf I , Msp I and Taq I . Results The 8 species of Trichosporon could be classified into 4 subgroups with rDNA-ITS-RFLP, while inter-species identification of all the 14 strains from 8 species of Trichosporon could be realized with rDNA-IGSl-RFLP. Also, those genotypes of T. asahii which had relative long phylogenic distance could even be discriminated with rDNA-IGSl-RFLP. Conclusion The rDNA-ITS/IGSl-RFLP analysis is expected to be used in rapid interspecific identification of genus Trichosporon.

Molecular identification of Trichogramma cacoeciae Marchal (Hymenoptera: Trichogrammatidae): a new record for Peru / Identificação molecular de Trichogramma cacoeciae Marchal (Hymenoptera: Trichogrammatidae): um novo registro para o Peru

Discovery of male morphological characters for species identification was a great improvement in Trichogramma systematic. However, not all species could be easily identified. In some cases, the lack of males (thelytokous status of species that carry the Wolbachia symbiont) made Trichogramma identification impossible. This problem was solved via antibiotic and heating treatments for elimination of the bacteria and allowing the production of males. The only Trichogramma species reported in which thelytoky is not induced by bacterial infection is T. cacoeciae, so here another means of species identification is needed. This species was identified based on the ITS2 (Internal transcribed spacer 2) sequence, a modern technique that has been proved useful in providing a reliable identification of Trichogramma species. Here we report the first occurrence of T. cacoeciae in Peru and we discuss its distribution in South America.

A história da taxonomia de Trichogramma teve um grande avanço com a descoberta dos caracteres morfológicos do macho. Entretanto, nem todas as espécies puderam ser facilmente identificadas. Em alguns casos, a identificação específica tornou-se impossível devido à ausência de insetos machos (condição das espécies telítocas infectadas por Wolbachia). Esse problema foi resolvido com a eliminação da bactéria por meio de tratamentos com uso de antibióticos e altas temperaturas. T. cacoeciae é a única espécie relatada até o momento cuja condição de telitoquia não é induzida por infeccção da bactéria Wolbachia, sendo necessário um novo método para identificação desta espécie. Resultados de alta confiabilidade têm sido obtidos na identificação específica de Trichogramma via sequenciamento da região ITS2 (Internal transcribed spacer 2). T. cacoeciae foi identificado com essa técnica e relatado pela primeira vez no Peru. A situação atual de T. cacoeciae na América do Sul é discutida.

DNA Typing of Sporothrix schenckii by Analysis of Ribosomal-DNA Regions / 中华皮肤科杂志

Objectives To identify genotypes of 31 Sporothrix schenckii (S.schenckii) strains by Southern blotting and to explore the relationship between genotypes and geographic distributions and clinical manifestations.Methods Total DNA was extracted by cetyltriethyl ammonium bromide (CTAB).The polymorphisms were detected by hybridization of ApaⅠ-digested S.schenckii genomic DNA with a probe amplified from the small-subunit rDNA and adjacent internal transcribed spacer (ITS) regions.The band patterns manifested by Southern blotting were employed to investigate genotypes of 31 strains of S.schenckii collected from five different areas in China.Results Of 31 strains of S.schenckii,15 individual patterns (DNA Type A-O) were recognized.Type A to C accounted for 51.61% of all strains.Conclusion The Southern blotting provides a highly sensitive and reliable means for DNA typing of S.schenckii.It is also found that there is an obvious correlation between DNA patterns and different geographic distribution and clinical manifestations.

A rapid molecular taxonomy technique on the bacteria genus and species by 16S rDNA and 16S-23S rDNA intergenic spacer regions sequences / 中华检验医学杂志

Objective To explore a rapid method for classification of microorganisms.Methods The electrophorese fingerprinting, direct sequence of 16S rDNA and 16S-23S rDNA ISR after PCR, multiplex PCR for 16S rDNA and antibiotic resistance genes, were utilized to explore fast approaches of extracting total DNA from different clinical specimens.Results The specific 16S-23S rDNA ISR fingerprinting fragments were shown on the genus or species level in bacteria and fungi.So fingerprinting can be used to identify pathogenic microorganisms, to differentiate the evolution relations or to set the phylogenetic tree by comparing their DNA banding patterns with those of standard strains (NCCLS). Multiplex PCR was able to examine the special genes of genus or species, mecA gene, TEM, SHV and CTX gene in staphylococcus and ESBLs(E.coli or K.pneumoniae) at the same time.Conclusion The part of 16S rDNA sequencing and 16S-23S rDNA ISR genotypes by gel electrophoreses were useful for bacterial species identification in addition, it was clearly more rapid and accurate than culture technique, and the large numbers of strains can easily be examined.Multiplex PCR could provide a good method for identification of microorganisms and analysis of antibiotic resistance at the same time.

Analyses of T-lymphocyte rDNA transcription in peripheral blood of patients with stomach-intestine tract malignant tumor / 中国病理生理杂志

AIM: To examine T-lymphocyte rDNA transcription activity in peripheral blood of patients with gastrointestinal maliganant tumor and to clarify its clinical significance.METHODS: T-lymphocyte rDNA transcription activity in peripheral blood of 48 cases of patients with stomach-intestine tract malignant tumor were measured.RESULTS: Before surgery, the T-lymphocyte rDNA transcviption activity was obviously lower than that after surgery, also lower than that of the normal control( P

Identification of Sporothrix schenckii Based on the Nucleotide Sequences in Internal Transcribed Spacer Region 2 of Ribosomal DNA Genes / 中华皮肤科杂志

Objective To study the molecular identification method of Sporothrix schenckii based on the nucleotide sequences in internal transcribed spacer region 2 of ribosomal DNA (rDNA) genes. Methods Species-specific primers were used to amplify the internal transcribed spacer region 2 of rDNA of 22 clinical isolates of Sporothrix schenckii and 12 strains of dematiaceous fungi. Totally 11 strains of Sporothrix schenckii were sequenced and analyzed, in which 1 strain came from the US and the others were isolated from different areas in China. A pair of species-specific oligonucleotide primers (SSP) were designed based on the ITS2 sequence. With the species-specific primers, rDNA of Sporothrix schenckii and dematiaceous fungi were amplified by PCR. Results Sequencing and analysis showed that internal transcribed spacer region 2 of rDNA gene was conservative in Sporothrix schenckii. A 300 bp fragment was obtained from 22 strains of Sporothrix schenckii, but not from the other species. Conclusions This method is specific, sensitive and reliable for the identification of Sporothrix schenckii and could be used for clinical molecular diagnosis.