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Home > Comparison of Xpert Mtb/Rif With Histology for the Detection of Mycobacterium Tuberculosis in Formalin Fixed Paraffin Embedded Tissues at Aga Khan University Hospital, Nairobi

Comparison of Xpert Mtb/Rif With Histology for the Detection of Mycobacterium Tuberculosis in Formalin Fixed Paraffin Embedded Tissues at Aga Khan University Hospital, Nairobi

Thesis Info

Author

Njoroge, Njau Allan

Department

Pathology (East Africa)

Program

MMed

Institute

Aga Khan University

Institute Type

Private

City

Karachi

Province

Sindh

Country

Pakistan

Thesis Completing Year

2018

Thesis Completion Status

Completed

Subject

Medicine

Language

English

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676728042565

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Background: Diagnosis of extrapulmonary tuberculosis (EPTB) continues to be a challenge due to the complexity of the causative organism and the wide array of pathologic features seen in this infection. A number of studies have shown polymerase chain reaction (PCR) for EPTB to be a feasible, sensitive and specific test for diagnosis of tuberculosis (TB) of which, the World Health Organisation (WHO) has given recommendations. As pertains EPTB, Xpert MTB/RIF may be used in place of conventional tests such as microscopy, histopathology and culture in lymph nodes and other tissues from patients suspected to have EPTB. It has been demonstrated that Xpert MTB/RIF can be used for fresh or frozen tissues specimens with good results. However, the use of formalin fixed paraffin embedded (FFPE) tissues, a widely available and rich source of clinical material, on the Xpert platform is yet to be described. Objectives: The aim of this study was to demonstrate the potential utility of Xpert MTB/RIF in the detection of Mycobacterium tuberculosis from FFPE tissues with histological features suggestive of tuberculosis. We compared Xpert MTB/RIF to histology for the detection of Mycobacterium tuberculosis from FFPE tissues. In those cases with a positive Xpert result, we determined the prevalence of rifampicin resistance in EPTB. Methods: Eighty randomly selected archived FFPE tissues exhibiting histological features suggestive of TB (necrotizing granulomatous inflammation, non-necrotizing granulomatous inflammation, chronic inflammation, necrotizing inflammation and suppurative inflammation) from January 1, though December 31, 2014 were retrieved. All the cases were subjected to microscopic evaluation of Haematoxylin and Eosin (H&E) stained and Ziehl-Neelsen (ZN) slides. With prior deparaffinization and lysis, all cases were also subjected to the Xpert MTB/RIF assay. Only 79 cases were included in the final analysis. This was after exclusion of one case due to an error in the Xpert MTB/RIF assay. The outcome measures were proportions of positively identified cases by each test. The data were analysed using chi - square test. Results: Xpert MTB/RIF assay detected 32.9% more cases than microscopy (53.2% versus 20.3%) which was statistically significant, (p= 0.002). None of the cases tested positive for rifampicin resistance. Seven cases however, had an indeterminate rifampicin resistance result. Conclusion: With prior deparaffinization and lysis, FFPE tissues can also be subjected to the Xpert MTB/RIF assay. A validation study to determine the clinical utility of this assay for FFPE tissues is recommended.
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Chapter 2: Services of Theologians of Sindh

Introduction

In the Indo-Pak sub-continent, Sindh is the first of the zones where the advent of Islām was the earliest. Historically, the scholars here did a great work of intellect and research. In the year 270 A. H/883A. D, due to internal disturbance, so many small states came into being. [1]

            Out of these, the state of Manṣūrah was taken over by the Ḥubārī tribe. Muslim ruler ‘Abdallāh bin ‘Umar Ḥubārī of Manṣūrah had sent a scholar to Hindū Rājāh of Alvar on his request who presented the translation of the Qur’ān in his court. This incident narrated by the famous historian Buzurg Bin Shehr Yār has also been endorsed by renowned historians of the sub-continent. [2]But nothing with certainty can be said about the symmetrical order and the dictation of this translation, however, it is certain that the honor of translating the Qur’ān the first of all lies with Sindh. [3]

            In the era of Arghaun and Tarkhān, Makhdūm Nūḥ Hālāe’ (d:998 A. H/1589A. D) properly translated the Qur’ān in Persian which has become available in secured form despite the varying times. [4]

            This translation, with the efforts and research of ‘Allāma Muṣṭafā Qāsmī (d:1424A. H/2003A. D) has been published by Sindh Literary Board Ḥyderābād. This translation was compiled even earlier than the translation of famous researcher Shāh Walī Allāh(d:1176A. H/1762A. D). In this regard, we are justified to opine that in the sub-continent the honor of the first translation in the Persian language also goes to Sindh. In that period, a movement among the Sindhī Scholars emerged that the Islamic literature and art be documented in the mother tongue Sindhī so that a...

عرب اسلامی روایت کے برصغیر پاک و ہند میں تفسیر نگاری پر اثرات: عہد رسالت تا خلافت عباسیہ کے تناظر میں اختصاصی مطالعہ

It is an established fact that the mainthrust driving force  of all Islamic disciplines is the personality of Prophet Muhammad (PBUH) who appeared in the Arab Peninsula, spreading the rays of divine wisdom throughout the globe. He emerged and prevailed the Prophetic message in such a vivid style that the whole humanity confessed his lasting impressions. The Indian sub-continent has also been one of the impressed territories despite of having no direct social, cultural or religious relationships, yet some approaches from Indian sub-continental Rajas and presentations of gifts to the Prophet (PBUH) have been recorded in the history. Historians have expressed the reality that before Muhammad bin Qasim, a numbers of companions of Prophet reached India and played a pivotal role in making the suitable ground for embracing Islam. Hence, the Arab epistemological tradition engraved in the core of Indian hearts which consequently, reappeared and emerged in the classical exegetical literature of sub-continental scholars, such as Shah Waliullah and his off shoots both in India and Pakistan. This paper has been specifically articulated to explore the Arab impression on exegetical writings in the sub-continent

Seroprevalence and Molecular Characterization of Infectious Bronchitis Virus Variants from Poultry in Pakistan

Infectious bronchitis virus (IBV) is incriminated in a variety of clinical conditions in poultry. IBV has a potential to mutate under field conditions and due to this multiple serotypes and variants of the IB virus circulates in commercial and backyard poultry. In the present study seroprevalence levels of different known serotypes of IBV such as, Mass-41, 4/91, D274, D1466, IT-02, D388 & D8880 were first determined in non IB-vaccinated poultry from different provinces of Pakistan during 2012 to 2015. The data showed high seroprevalence of multiple serotypes of IBV indicating high level of diversity in the circulating serotypes/variants of IBV in this country. In addition to this, a post-IBV vaccination base line was developed by sero-monitoring among healthy poultry in response to IBV vaccines, providing a permanent reference for future monitoring of post-vaccination antibody titers For further IBV investigations, different diagnostic techniques to be used in this study were optimized in this study. Moreover, studies regarding the determination of tissue tropism of one of the new IBV isolates along with evaluation of its co-infection potential with Avian Influenza virus H9N2 and ORT were also carried out. For the detection and typing of locally circulating Pak-IBV isolates following techniques were first optimized including, haemagglutination (HA), haemagglutination inhibition (HI), Indirect-Enzyme linked immunosorbent assay (ELISA), restriction fragment length polymorphism (RFLP), reverse transcriptase polymerase chain reaction (RT-PCR), real time reverse transcriptase polymerase chain reaction (QRT-PCR), virus neutralization (VN). Using these techniques, a total of 3187 clinical samples were processed for IBV detection, out of this 871 were IBV positive. Moreover, subtype detection revealed that 45.2% was Mass-41, 51.3% was IBV serotype 793-B and 3.4% were variants or un-identified. Furthermore, 871 RT-PCR positive samples were propagated upon in-ovo inoculation in specific pathogen free (SPF) embryonated chicken eggs. Out of this 55 IBV isolates were subjected to RFLP analysis that grouped the isolates into three segments, first was designated as 4/91 like group, second was designated as Mass-41 like group and the third was designated as IBV variant. The sequence and phylogenetic analysis of three IBV isolates from each RFLP group revealed that the first isolate, Pak IBV-786, shared sequence homology of the range of 25 99.1%-99.5% with 4/91 like strains from China, India, Russia, Morocco, Japan and Iran or GI-13 IBV lineage. The second isolate, Pak IBV-1113 shared 98% sequence of its sequence with IBV vaccine strains of Ma5 and M41 from Brazil, India, USA, Egypt, China, Iran, Thailand and Poland. The third and new Pak isolate, IBV-973, shared 91-93% of its sequence with the Indian strains of IBV earlier reported in India only, of GI-24 lineage. This strain of IBV variant has been first time reported from commercial poultry in Pakistan and its subsequent molecular characterization revealed that this virus is in fact a new serotype of IBV earlier only reported from India. Pathogenesis and co-infection studies on the isolate Pak-973 further highlighted biological characteristics of the new Pak-variant, which led us to believe that this variant may be contributing significantly towards the development of super complex of Respiratory Tract Infection, with or without the involvement of AIV H9N2. The sequence and phylogenetic analysis of different Pak IBV isolates reflected here that the genome of IBV is under a continuous process of evolution, due to point mutations, selective pressure (vaccine) and recombination events. So as like other RNA viruses, the IBV control is most likely to succeed upon using serotype specific vaccines (Homologous vaccines), as carried out elsewhere. It would, therefore be highly appropriate to recommend the incorporation of strain Pak-973 in commercial poultry vaccines being used in this country. INDEX WORDS: Infectious bronchitis virus, Pak-variants, Spike glycoprotein, RFLP, Real time RT-PCR, Co-infection, Tissue tropism