Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis

OBJECTIVES

The aim of this study is to investigate the clinical usefulness of metagenomic Next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) samples to discriminate pulmonary tuberculosis (PTB) from Non-TB community-acquired pneumonia (CAP) in PTB suspects.

METHODS

We investigate the performance of mNGS on BALF samples from 110 PTB suspects, in comparison with conventional microbiological testing (solid media culture, acid-fast bacilli staining (AFS), Xpert) of BALF or sputum samples and final clinical diagnosis.

RESULTS

We finally clinically diagnosed 48 cases of pulmonary tuberculosis patients and 62 cases of non-tuberculosis patients. Comparing to the final clinical diagnosis, mNGS produced a sensitivity of 47.92%, which was similar to that of Xpert (45.83%) and culture (46.81%), but much higher than that of AFS (29.17%) for TB diagnosis in BALF samples. Apart from detecting Mycobacterium tuberculosis, mNGS also identified mixed infections in PTB patients, including 3 fungal cases and 1 bacteria case. Meanwhile, mNGS efficiently identified 14 of 22 (63.63%) cases of non-tuberculous mycobacteria (NTM), 7 cases of fungi, 1 case of viral infection, and other common bacterial pathogens in Non-PTB group. Finally, mNGS identified 67.23% infection cases within 3 days, while the conventional methods identified 49.58% infection cases for over 90 days.

CONCLUSION

Our data show that mNGS of BALF represents a potentially effective tool for the rapid diagnosis of PTB suspects.

[Diagnostic value of serum miRNA let-7a for laryngeal carcinoma and effects of let-7a on proliferation and apoptosis of laryngeal carcinoma cells]

Objective: To investigate the diagnostic value of serum miRNAlet-7a in laryngeal carcinoma and the effect of let-7a on proliferation and apoptosis of laryngeal carcinoma cells. Methods: Real-time quantitative PCR was used to determine the expression level of serum miRNAlet-7a. The miRNA let-7a mimetic was synthesized and transiently transfected into the laryngeal carcinoma Hep-2 cell line by cationic liposome method. The effects of up-regulation of let-7a expression on laryngeal cancer Hep-2 cells were detected by FCM and MTT assays,respectively. The association of let-7a levels with laryngeal cancer and the diagnostic value for laryngeal cancer were analyzed. Measurement data were taken by t test or analysis of variance; Counting data were analyzed by χ(2) test and Fisher exact probability method. The receiver operating characteristic curve was used to analyze the diagnostic value of let-7a for laryngeal cancer. Results: The relative expression of serum let-7a in healthy subjects was significantly higher than that in patients with laryngeal cancer (0.931±0.094) vs (0.380±0.113) (t=26.507,P<0.01). The relative expressions of serum let-7a in patients with laryngeal cancer before and after surgery were (0.380±0.113) vs(0.493±0.164),with significant difference (t=3.848,P<0.01).The relative expression of serum let-7a was related to lymph node metastasis (t=2.946, P<0.01). There was a positive correlation between the relative expression of let-7a in laryngeal carcinoma and that in serum (r=0.466,P=0.003). After transfection of let-7a mimics, Hep-2 cells showed an increased significant increase in the expression of let-7a (P<0.01), proliferation (P<0.01) and apoptosis (P<0.01). ROC curve analysis showed that the best critical value for relative expression of let-7a in the diagnosis of laryngeal carcinoma was 0.557 with a sensitivity of 0.794,a specificity of 0.727,an area under curve(AUC) of 0.859,and a 95%CI of 0.773-0.926. Conclusions: miRNA let-7a can inhibit the proliferation of laryngeal carcinoma Hep-2 cells and promote apoptosis. Serum let-7a is down-regulated in patients with laryngeal cancer and the level of let-7a is related to lymph node metastasis,which would help early diagnosis and postoperative disease monitoring of laryngeal cancer,but further research is needed.

Development and characterization of microsatellite loci in Excentrodendron hsienmu (Chun & How) H.T. Chang& R.H. Miau

Microsatellite markers were isolated using dual-suppression-PCR for the endangered species Excentrodendron hsienmu (Tiliaceae) to evaluate the genetic diversity and population structure of this species. A total of 11 polymorphic microsatellite loci were characterized in E. hsienmu. The number of alleles per locus ranged from 2 to 9, with an average of 5.27. The expected heterozygosity value ranged from 0.053 to 0.780, with an average of 0.568 and the observed heterozygosity value ranged from 0 to 0.595, with an average of 0.268. The polymorphic information content value ranged from 0.051 to 0.740, with an average of 0.521. These newly designed markers will be of great potential significance and profound influence in future research related to the genetic diversity, population structure, and patterns of gene flow of this species, which will contribute to the implementation of conservation and management strategies for this species.

First Report of Herbaspirillum rubrisubalbicans Causing Mottled Stripe Disease on Sugarcane in China

Narrow, red stripes were observed on leaves and sheaths of sugarcane in 2007 in DanZhou County of Hainan Province and XuWen County of GuangDong Province, China. Stripes were parallel to the leaf veins. Some stripes were short (2 to 10 cm) and some were >1 m long, extending from the base of leaves. Width of the stripes was 2 to 4 mm. Symptoms varied with the cultivar. Cv. Taiwang 25, which was the most affected, exhibited red stripes and stalk death from the apex. Cvs. Taiwang 26 and Guang Dong 00236 were slightly affected with only red stripes. Symptoms on cv. Taiwang 22 were mottled stripes. Severe losses were observed in the infected fields that were planted with cv. Taiwang 25, but there were no obvious losses in fields planted with the other three cultivars. Isolations were made from 10 individual plants from different cultivars and provinces that had red stripes, two of which also had apex death. Five independent bacterial isolates were obtained from tissue showing the red stripe symptoms on potato dextrose agar medium. The percentage of positive samples was 50%. No bacteria were obtained from necrotic apex tissue. Bacterial cells were 0.92 to 1.55 × 0.20 to 0.22 μm slightly curved rods that were motile with one to two polar flagella. Colonies on nutrient agar were 2 to 3 mm in diameter, circular, smooth, entire, and milky white. Colonies on King's medium B were nonfluorescent under 365-nm UV light. Five bacterial strains were inoculated by injecting bacterial suspensions (1 × 10⁸ CFU/ml) into the base of the leaves of 6-month-old cv. Taiwang 25 plants (1). Red stripes appeared 7 to 10 days after inoculation and bacteria were reisolated. The reisolated bacteria were identical to the original strains in colony morphology and 16S rDNA sequence. A hypersensitive response appeared within 24 h when 1 × 10⁸ CFU/ml bacteria suspensions were infiltrated into tobacco leaves. Approximately 1,000-bp DNA fragments were amplified with universal primers UP1 (5'-TACGTGCCAGCAGCCGCGGTAATA-3') and UP2 (5'-AGTAAGGAGGGTATCCAACCGCA-3') (3). Primers UP1 and UP2 are complementary to nucleotide sequence 509 to 523 and 1541 to 1522, respectively, of the Escherichia coli 16S rDNA gene. The fragment amplified by these primers was approximately 1,032 bp. The 16S rDNA sequences of the five strains were deposited in GenBank as Accession Nos. GQ476791-5. They all shared 99% nucleotide identity with the type strain of Herbaspirillum rubrisubalbicans (GenBank No. AJ238356.1). All five strains were identified as H. rubrisubalbicans on the basis of 16S rDNA sequence and pathogenicity to sugarcane, and the disease was identified as mottled stripe disease (2). Since we were not able to isolate bacteria from necrotic apex tissue, this symptom on cv. Taiwang 25 may not be related to the H. rubrisubalbicans infection. To our knowledge, this is the first report of mottled stripe disease in China. References: (1) H. M. A. EI-Komy et al. Folia Microbiol. 48:787, 2003. (2) A. S. Saumtally et al. A Guide to Sugarcane Diseases. P. Rott et al., eds. CIRAD and ISSCT, Montpellier, France, 2000. (3) Yan Zhi Yong et al. Chin. J. Epidemiol. 24:296, 2003.

Measurements of the continuum R(uds) and R values in e(+)e(-) annihilation in the energy region between 3.650 and 3.872 GeV

We report measurements of the continuum R(uds) near the center-of-mass energy of 3.70 GeV, the R[uds(c)+psi(3770)](s) and the R(had)(s) values in e(+)e(-) annihilation at 68 energy points in the energy region between 3.650 and 3.872 GeV with the BES-II detector at the BEPC Collider. We obtain the R(uds) for the continuum light hadron (containing u, d, and s quarks) production near the DD threshold to be R(uds)=2.141+/-0.025+/-0.085.

Search for invisible decays of eta and eta' in J/psi --> phi eta and phi eta'

Using a data sample of 58 x 10(6) J/psi decays collected with the Beijing Spectrometer II detector at the Beijing Electron Positron Collider, searches for invisible decays of eta and eta' in J/psi to phi eta and phi eta' are performed. The phi signals, which are reconstructed in K+K- final states, are used to tag the eta and eta' decays. No signals are found for the invisible decays of either eta or eta', and upper limits at the 90% confidence level are determined to be 1.65 x 10(-3) for the ratio B(eta-->invisible)/B(eta --> gamma gamma) and 6.69 x 10(-2) for B(eta' --> invisible)/B(eta' --> gammagamma). These are the first searches for eta and eta' decays into invisible final states.

Observation of a broad 1-- resonant structure around 1.5 GeV/c2 in the K+K- mass spectrum in J/psi-->K+K-pi0

A broad peak is observed at low K+K- invariant mass in J/psi-->K+K-pi(0) decays found in a sample of 5.8x10(7) J/psi events collected with the BESII detector. The statistical significance of the broad resonance is much larger than 5sigma. A partial wave analysis shows that the J;{PC} of this structure is 1--. Its pole position is determined to be [1576(-55)(+49)(stat)-91+98(syst)] MeV/c(2)-i/2[818(-23)(+22)(stat)-133+64(syst)] MeV/c(2). These parameters are not compatible with any known meson resonances.

Measurements of the branching fractions for psi(3770)-->D(0)D[over ](0), D+D-, DD[over ], and the resonance parameters of psi(3770) and psi(2S)

We measure the branching fractions for psi(3770)-->D(0)D[over ](0), D+D-, DD[over ], and non-DD[over ] to be (46.7+/-4.7+/-2.3)%, (36.9+/-3.7+/-2.8)%, (83.6+/-7.3+/-4.2)%, and (16.4+/-7.3+/-4.2)%, respectively. The resonance parameters of psi(3770) and psi(2S) are measured to be M_(psi(3770))=3772.2+/-0.7+/-0.3 MeV, Gamma_(psi(3770))(tot)=26.9+/-2.4+/-0.3 MeV, and Gamma_(psi(3770))(ee)=251+/-26+/-11 eV; M_(psi(2S))=3685.5+/-0.0+/-0.3 MeV, Gamma_(psi(2S))(tot)=331+/-58+/-2 keV, and Gamma_(psi(2S))(ee)=2.330+/-0.036+/-0.110 keV. We also measure the light hadron R value to be R(uds)=2.262+/-0.054+/-0.109 in the energy region from 3.660 to 3.872 GeV.

Observation of a near-threshold enhancement in the omega(phi) mass spectrum from the doubly OZI-suppressed decay J/psi-->gamma(omega)phi

An enhancement near threshold is observed in the omega(phi) invariant mass spectrum from the doubly Okubo-Zweig-Iizuka-suppressed decays of J/psi-->gamma(omega)phi, based on a sample of 5.8 x 10(7) J/psi events collected with the BESII detector. A partial wave analysis shows that this enhancement favors JP=0+, and its mass and width are M=1812(+19)(-26)(stat)+/-18(syst) MeV/c2 and Gamma=105+/-20(stat)+/-28(syst) MeV/c2. The product branching fraction is determined to be B(J/psi-->gammaX)B(X-->omega(phi))=[2.61+/-0.27(stat)+/-0.65(syst)]x10(-4).

Observation of a resonance in Chi(1835) in J/psi --> gammapi+ pi- eta-

The decay channel J/psi --> gamma(pi)(+)pi(-)eta is analyzed using a sample of 5.8 x 10(7) J/psi events collected with the BESII detector. A resonance, the Chi(1835), is observed in the pi(+)pi(-)eta invariant-mass spectrum with a statistical significance of 7.7 sigma. A fit with a Breit-Wigner function yields a mass M = 1833.7 +/- 6.1(stat) +/- 2.7(syst) MeV/c(2), a width Tau = 67.7 +/- 20.3(stat) +/- 7.7(syst) MeV/c(2), and a product branching fraction B(J/psi --> gammaChi) . B(Chi --> pi(+)pi(-)eta) = [2.2 +/- 0.4(stat) +/- 0.4(syst)] x 10(-4). The mass and width of the Chi(1835) are not compatible with any known meson resonance. Its properties are consistent with expectations for the state that produces the strong pp mass threshold enhancement observed in the J/psi --> gammapp process at BESII.