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Home > Comparison of the Sensitivity of Biomarker Based Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Maldi-Tof Ms and Conventional Methods in the Identification of Clinically Relevant Bacteria and Yeast

Comparison of the Sensitivity of Biomarker Based Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Maldi-Tof Ms and Conventional Methods in the Identification of Clinically Relevant Bacteria and Yeast

Thesis Info

Author

Kassim, Ali Abdow

Department

Pathology (East Africa)

Program

MMed

Institute

Aga Khan University

Institute Type

Private

City

Karachi

Province

Sindh

Country

Pakistan

Thesis Completing Year

2017

Thesis Completion Status

Completed

Subject

Medicine

Language

English

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676728041474

Similar


Background: MALDI-TOF MS is an analytical method that has recently become integral in the identification of microorganisms in clinical laboratories. It relies on databases that majorly employ pattern recognition or fingerprinting. Biomarker based databases have also been developed and there is optimism that these may be superior to pattern recognition based databases. This study compared the performance of ribosomal biomarker based MALDI-TOF MS and conventional methods in the identification of selected bacteria and yeast. Methodology: The study was a cross sectional study carried out in collaboration with the Swiss Tropical and Public Health Institute, Switzerland and Mabritec laboratory, Riehen, Switzerland. Clinically relevant bacteria and yeasts identified from clinical specimens submitted to the Aga Khan University Hospital, Nairobi (AKUH, N) laboratory were included in the study. The processing of the clinical specimens and identification of the isolates using conventional Vitek 2 automated system and serotyping was performed at AKUH, N while the identification of the isolates using MALDI-TOF MS and analysis of spectra using SARAMISTM and PAPMIDTM databases was performed at Mabritec laboratory, Riehen, Switzerland. Comparison of sensitivities was then carried out using Pearson Chi-Square test or Fischer’s exact test and P value of < 0.05 was considered statistically significant. Secondary outcomes analyzed include the proportion of major and minor errors reported in percentages. Results: Of the 386 isolates MALDI-TOF MS and conventional methods identified 97.6 % and 95.8 % (p = 0.155) to the genus level and 97.5 % and 87.3 % (p < 0.001) to the species level respectively. Biomarker based MALDI-TOF MS was significantly superior to Vitek 2™ in the identification of Gram negative bacteria and Gram positive bacteria to the species level. PAPMIDTM correctly identified isolates of Klebsiella variicola and Acinetobacter genomospecies 13BJ/14TU that were misidentified by SARAMISTM and Vitek 2™. For the Gram positive bacteria, significant difference was observed in the identification of Coagulase negative Staphylococcus (p < 0.001) and Enterococcus (p = 0.008). Significant difference was also observed between serotyping and MALDI-TOF MS (p = 0.005) and this was attributed to the lack of identification of Shigella species by MALDI-TOF MS. No significant difference was observed in the identification of yeast however some species of Candida were unidentified by MALDI-TOF MS. Conclusion: Biomarker based MALDI-TOF MS had good performance in a clinical laboratory setting with high sensitivities in the identification of clinically relevant microorganisms.
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ساون

ساون
ساون ماہ دا بدل آیا دل ہویا مسرور
سجن بھاویں جتھے ہووے ملنا بہت ضرور

دلبر سوہنا ملن نہ آوندا
دل کملا اے بڑا ستوندا
کدی تاں سوہنیا کرم کموندا
دل ملنے لئی ہے مجبور

ساری دنیا موج پئی کردی
مینوں تانگ لگی دلبر دی
میں سجناں دا پانی بھردی
پھراں میں جہلم تے پسرور

جے دل حجرہ صاف ہو جاوے
دلبر سوہنا پھیرا پاوے
گھر بیٹھیاں نوں مکھ وکھاوے
ویکھ کے نین ہوون مخمور

جدوں میں من وچ جھاتی پائی
صورت دلبر نظر سی آئی
دل دی ساری پیاس بجھائی
میرے غم ہوئے سب دور

دلبر نوں میں جان نہ دیساں
منتاں کرساں رات رہیساں
زخم دلے دے کھول وکھیساں
مینوں چھڈ نہ جان حضور

قادریؔ کدی نہ یاری چھوڑیں
کسے بندے دا دل نہ توڑیں
ہر دم یار دی مرضی لوڑیں
بھاویں ہوویں چکنا چور

صلح حدیبیہ: آنحضرت کی ﷺ سیاسی، معاشرتی اور دفاعی حکمت عملی

Hazrat Muhammad (SAW) is the last Apostle to human beings. He was gifted with a divine Deen having complete code of life. Every field of life has been discussed in the Holy Quran and Sunnah of the Prophet r. As an Apostle, head of the state and army commander, He guided the mankind and provided an excellent example in all the perspectives of life. As a commander of the Islamic forces, the Holy Prophet r fought twenty seven Ghazwat after migration to Madina. In Zeqaida 6 AH, during the pact of Hudaibia a complete turn was taken by Muslims. After this event, the Muslim army role changed to offensive rather than defensive. Immediately, after the pact, the Holy Prophet r attacked on Khyber in Muharram 7th AH, while the whole Hijaz region was captured during the Ghazwa Fath-i-Makkah. In this article, the strategy and tactics employed by the Holy Prophet r during Hudaibia truce have been discussed. These tactics are useful and beneficial in modern era warfare also. As an ideal for all the Ummah, lessons should be extracted by the commanders to defend their motherland and ideological boundries.

Characterization of Deep Level Defects in N-Type Zinc Oxide Layers Grown by Hydrothermal Technique

Zinc oxide (ZnO) is a promising wide-bandgap semiconductor due to its favorable properties for a variety of demanding device applications such as UV light emitters/detectors, high-power and high-temperature devices. The presence of defects in the material can considerably change the electrical properties of the semiconductors. However, recently it has been found that the terminated face of the material significantly alter the characteristics of such devices. The defects in ZnO have been studied in last decades, but no clear consensus has been made. This dissertation investigates the electrical properties of defects in ZnO grown by hydrothermal and molecular beam epitaxy techniques using deep level transient spectroscopy (DLTS). Among the growth techniques available to grow the thin film, the hydrothermal is one of the most cheap and user friendly technique. DLTS provides a sensitive method for identifying defects and for determining their parameters. The main findings are as follow: A. Several circular Schottky contacts (1mm diameter) with Pd metal on the Znface and O-face on n-type ZnO grown by hydrothermal and Ohmic contact of nickel-gold on the backside were deposited by e-beam technique. The asobtained samples were labeled as group A and B samples, respectively. The present literature on n-type ZnO has highlighted a defect, labeled as E3 irrespective of growth technique, which is also studied thoroughly in this research project. The respective summary of each group A and B of samples is explained below: · DLTS has been carried out on the group A samples to study deep level defects. Its result showed two electron trap level E1 having activation energy Ec-0.22 ±0.02 eV and E2 with activation energy Ec-0.49 ±0.05 3 eV. E1 level has time-delayed transformation of shallow donor defects zincinterstitial and vacancyoxygen (Zni-VO) complex. It is observed through X-ray differaction that the preferred direction of ZnO growth is along (10 1 0) plane i.e. VO-Zni complex, assuming that under favourable condition (Zni-VO) complex is transformed into a zinc antisite (ZnO). Consequently, the trap concentration increases with decreasing free carrier concentration. Hence, the ZnO is correlated to E1 level demonstrating the increase in concentration. · Several renowned research groups have revealed different points defects in bulk ZnO like naming oxygen vacancy, zinc interstitial, and/or zinc antisite. These defects having activation energy (free carrier concentration) in the range of 0.32–0.22 eV (1014 -1017 cm-3 ) below conduction band. The results of group A and B samples also showed activation energy (free carrier concentration) as observed by other renowned research groups. This result is due to activation energy of the level while it is not conceivable by with Vincent et al.,[ J. Appl. Phys. 50 (1979) 5484]. They believed that data should be carefully interpreted obtaining by capacitance transient measurement of diodes having carrier concentration greater than 1015 cm -3 . Thus the influence of background free-carrier concentration, ND induced field on the emission rate signatures of an electron point defect in ZnO Schottky devices has been studied by using deep level transient spectroscopy. Many theoretical models were tested on the experimental data to understand the mechanism. Our findings were supported by PooleFrenkel model based on Coulomb potential. It is revealed by 4 investigation that Zn related charged impurities were found to be responsible for electron trap. Results were also tested through qualitative measurements like current-voltage and capacitance-voltage measurements. B. Several Schottky contacts of 1mm diameter with silver were prepared on ZnO grown by molecular beam epitaxy. These samples were labeled as group C samples, DLTS measurements revealed a hole trap exhibiting metastability effect in the emission rates of trap with storage time. We determined that hole trap transfers from one configuration to other with storage time. As a result the activation energy of the acceptor level varied in the range of 0.31 eV to 0.49 eV above the valance band at different measurement time. Impurities cannot be removed in the growth procedure. SIMS results showed the presence of nitrogen. During the growth process nitrogen occupies O site and produces Zn-N complex. But Zn-N bond is not stable because of its large bonding energy and consequently results into metastable nature of the defect. All experimental findings and available literature support the conclusion that the observed hole trap arise from Zn-N complex. C. The ZnO nanorods were grown on glass substrate coated with different metal (Ni, Al, Ag and Au) by aqueous chemical growth. These samples were labeled as D, E, F and G, respectively. The structural properties of ZnO nanorods were investigated by X-Ray diffraction (XRD) and scanning electron microscopy (SEM). The intensity of ZnO (0 0 2) diffraction peak in X-ray diffraction pattern is maximum of sample D because of nucleation of Ni metal coated on substrate. SEM measurements strongly support our observation that thin layer Ni metal increases the growth of nanorods.