• Annals of Clinical Microbiology
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• v.18 no.2
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• pp.37-43
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• 2015

Background: Tuberculosis is globally the most important cause of death from single pathogen. Rapid and accurate identification of mycobacteria is essential for the control of tuberculosis. We evaluated a fluorescence in situ hybridization (FISH) method using peptide nucleic acid (PNA) probes for the differentiation of Mycobacterium tuberculosis complex (MTB) and nontuberculous mycobacteria (NTM) in direct smears of sputum specimens. Methods: The cross-reactivity of MTB- and NTM-specific PNA probes was examined with reference strains of M. tuberculosis ATCC 13950, Mycobacterium kansasii ATCC 12479, Mycobacterium fortuitum ATCC 6841, several clinical isolates of mycobacteria (Mycobacterium abscessus, Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium gordonae and Mycobacterium chelonae), and 11 frequently isolated respiratory bacterial species other than mycobacteria. A series of 128 sputa (89 MTB culture positive, 29 NTM culture positive, and 10 under treatment culture negative) with grades of trace to 4+ were used to evaluate the performance of the method. Results: The MTB- and NTM-specific PNA probes showed specific reactions with the reference strains of MTB and M. kansasii and clinical isolates of mycobacteria except M. fortuitum ATCC 6841, and no cross-reactivity with other tested bacteria. The PNA probe-based FISH assay for detection of MTB had a sensitivity and specificity of 100%, respectively. The sensitivity and specificity of the NTM-specific PNA probe was 100%. The smear grades of the PNA FISH test were same as with those of the fluorescence AFB stain in 2+ or higher grade. Conclusion: Detection and differentiation based on PNA FISH is sensitive and accurate for detecting mycobacteria and for differentiating MTB from NTM in clinical sputum smears.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.5
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• pp.853-860
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• 2012

To estimate potential use of fly ash in reducing $CH_4$ and $CO_2$ emission from soil, $CH_4$ and $CO_2$ fluxes from a paddy soil mixed with fly ash at different rate (w/w; 0, 5, and 10%) in the presence and absence of fertilizer N ($(NH_4)_2SO_4$) addition were investigated in a laboratory incubation for 60 days under changing water regime from wetting to drying via transition. The mean $CH_4$ flux during the entire incubation period ranged from 0.59 to $1.68mg\;CH_4\;m^{-2}day^{-1}$ with a lower rate in the soil treated with N fertilizer due to suppression of $CH_4$ production by $SO_4^{2-}$ that acts as an electron acceptor, leading to decreases in electron availability for methanogen. Fly ash application reduced $CH_4$ flux by 37.5 and 33.0% in soils without and with N addition, respectively, probably due to retardation of $CH_4$ diffusion through soil pores by addition of fine-textured fly ash. In addition, as fly ash has a potential for $CO_2$ removal via carbonation (formation of carbonate precipitates) that decreases $CO_2$ availability that is a substrate for $CO_2$ reduction reaction (one of $CH_4$ generation pathways) is likely to be another mechanisms of $CH_4$ flux reduction by fly ash. Meanwhile, the mean $CO_2$ flux during the entire incubation period was between 0.64 and $0.90g\;CO_2\;m^{-2}day^{-1}$, and that of N treated soil was lower than that without N addition. Because N addition is likely to increase soil respiration, it is not straightforward to explain the results. However, it may be possible that our experiment did not account for the substantial amount of $CO_2$ produced by heterotrophs that were activated by N addition in earlier period than the measurement was initiated. Fly ash application also lowered $CO_2$ flux by up to 20% in the soil mixed with fly ash at 10% through $CO_2$ removal by the carbonation. At the whole picture, fly ash application at 10% decreased global warming potential of emitted $CH_4$ and $CO_2$ by about 20%. Therefore, our results suggest that fly ash application can be a soil management practice to reduce green house gas emission from paddy soils. Further studies under field conditions with rice cultivation are necessary to verify our findings.

• Tuberculosis and Respiratory Diseases
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• v.59 no.5
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• pp.522-529
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• 2005

Background : Several national societies have published guidelines for empirical antimicrobial therapy in patients with severe community-acquired pneumonia (SCAP). This study investigated the etiologies of SCAP in the Asan Medical Center and assessed the relationship between the initial empirical antimicrobial regimen and 30 day mortality rate. Method : retrospective analysis was performed on patients with SCAP admitted to the ICU between March 2002 and February 2004 in the Asan Medical Center. The basic demographic data, bacteriologic study results and initial antimicrobial regimen were examined for all patients. The clinical outcomes including the ICU length of stay, the ICU mortality rate, and 30 days mortality rates were assessed by the initial antimicrobial regimen. Results : One hundred sixteen consecutive patients were admitted to the ICU (mean age 66.5 years, 81.9 % male, 30 days mortality 28.4 %). The microbiologic diagnosis was established in 58 patients (50 %). The most common pathogens were S. pneumoniae (n=12), P. aeruginosae (n=9), K. pneumonia (n=9) and S. aureus (n=8). The initial empirical antimicrobial regimens were classified as: ${\beta}$-lactam plus macrolide; ${\beta}$-lactam plus fluoroquinolone; anti-Pseudomonal ${\beta}$-lactam plus fluoroquinolone; Aminoglycoside combination regimen; ${\beta}$-lactam plus clindamycin; and ${\beta}$-lactam alone. There were no statistical significant differences in the 30-day mortality rate according to the initial antimicrobial regimen (p = 0.682). Multivariate analysis revealed that acute renal failure, acute respiratory distress syndrome and K. pneumonae were independent risk factors related to the 30 day mortality rate. Conclusion : S. pneumoniae, P. aeruginosae, K. pneumonia and S. aureus were the most common causative pathogens in patients with SCAP and K. pneumoniae was an independent risk factor for 30 day mortality. The initial antimicrobial regimen was not associated with the 30-day mortality.