Τα τελευταία χρόνια παρατηρείται παγκοσμίως επιδείνωση των επιδη­μιο­λογικών δεικτών της φυματίωσης με αποτέλεσμα την αναζοπύρωση του διε­θνούς ενδιαφέροντος έρευνας που αφορά τη διακοπή μετάδοσης της αλυσί­δας των μυκοβακτηριδιακών λοιμώξεων. Κύριο στοιχείο ελέγχου και περιστολής της νόσου αποτελεί η αναζήτηση και θεραπεία των πασχόντων με θετικά πτύελα έτσι ώστε να καταστεί δυνατή η διακοπή μετάδο­σης των μυκοβακτη­ριδίων. Τα μικρά ποσοστά της άμεσης μικροβιο­λο­γι­κής επιβεβαίω­σης μιας κλινικής διάγνωσης, η καθυστέρηση των καλλιεργειών λόγω μεγάλου χρόνου επώασης καθώς και το χρονοβόρο και ανεπαρκές των κλασσικών μεθόδων ελέγχου ευαισθησίας στα διάφορα αντιφυματικά φάρμα­κα επιβάλ­λουν συνεχή έρευνα προς ανεύρεση γρήγορων και ευαίσθητων διαγνωστικών μεθόδων. Στην παρούσα μελέτη μελετήθηκαν 3.500 δείγματα προερχόμενα από ασθε­νείς της πενταετίας 1999-2003 που προσήλθαν στο Πανεπιστημιακό Γενικό Νοσοκομείο Πατρών καθώς και στο Ειδικό Νοσοκομείο Νοσημάτων Θώ­­ρακος Δυτικής Ελλάδος με σκοπό την ανεύρεση μυκοβακτηριδίων (Myco­bacterium spp.). Η μελέτη περιελάμ­βα­νε: α) άμεσο έλεγχο σε παρασκεύα­σμα μετά από οξεάντο­χη χρώση Ziehl-Neelsen (ΖΝ) για ανεύρεση οξεά­ντοχων και αλκοολάντοχων βακτηρίων (Acid Fast Bacteria –AFB) σε ποι­κίλα δείγματα του αναπνευ­στικού, αλλά και από άλλα στείρα υγρά σώ­μα­τος, και β) τη μο­ριακή μέθοδο COBAS AMPLICOR αλυσιδωτή αντίδραση πολυμεράσης (CA PCR). Η ευαισθησία, η ειδικότητα, η θετική και αρνητική προγνωστική αξία της CA PCR καθο­ρίστηκε μεταξύ AFB-θετικών και AFB-αρνητικών δειγ­μάτων. Υψηλή ευαισθησία της CA PCR παρατηρήθηκε μεταξύ όλων των AFB-θετικών δειγμάτων, ενώ τα δείγματα πτυέλων που ελήφθησαν μετά από βρογχοσκό­πη­ση (ΜΤΒ-πτύελα) θεωρήθηκαν τα πλέον κατάλληλα δείγματα με ευαισθη­σία 70% και ειδικότητα 98,6% μεταξύ των AFB-αρνητικών δειγμάτων. Η αύξηση τα τελευταία χρόνια της ανθεκτικότητας στελεχών του Μ. tuberculosis καθιστά αναγκαία την καλλιέργεια και την ευαισθησία στα αντιφυ­μα­­τικά φάρ­μακα. Για το σκοπό αυτό, μετά από ειδική επεξεργασία των κλινι­κών δειγ­μά­των (ρευστοποίηση και εμπλουτισμό) σύμφωνα με το πρωτόκολλο της εται­ρείας Becton Dickinson BBL MycoPrep, ακολούθησε καλλιέργεια η οποία έγινε ταυτόχρονα με δυο μεθόδους: α) σε στερεό θρεπτικό υλικό Löwentein-Jensen (L-J BioMerieux, SA Lyon, France), και β) σε φιαλίδια BACTEC MYCO/F Becton-Dickinson για γρήγορη ανί­χνευση με το αυτόματο σύ­στημα BACTEC 9000 ΜΒ. Θετικές καλλιέργειες προερχόμενες και από τις δύο μεθό­δους επιβεβαιώθηκαν με τρεις τρόπους: α) χρώση (Ζ-Ν) του παρασκευά­σματος για οξεάντοχα και αλκοολάντοχα βακτηρίδια (AFB) β) ανακαλλιέργεια σε L-J και γ) CA PCR. Ακολούθησε ταυτο­ποίηση ειδών Mycobacterium spp: α) με βιο­χημικές δοκιμασίες (παραγωγή νιασίνης – παραγωγή θερμοανθεκ­τι­κής καταλάβης), και β) με μεθόδους μοριακής βιολογίας (PCR και υβριδισμό Genotype Mycobacteria). Σε 88 ΜΤΒ απομονωθέντα στελέχη από διαφο­ρε­τι­κούς ασθενείς τα οποία ταυτοποιήθηκαν με PCR και υβρι­δι­σμό, εφαρμό­στηκε δοκιμασία ευαισθησίας στα τέσσερα πρώτης επιλο­γής αντιφυματικά φάρμακα (INH, RIF, STR, EMB) με τρεις διαφορετικές μη αυτόματες μεθόδους: τη μέθοδο αναλογιών σε άγαρ (ΜΟΡ), την MGIT και το E-test. Καλή συμφωνία αποτελεσμάτων σημειώθηκε μεταξύ E-test και ΜΟΡ για την ΙΝΗ και RIF, ενώ μεταξύ των μεθόδων MGIT και ΜΟΡ παρατηρήθηκε καλή συμφωνία για την ΙΝΗ, RIF και STR. Έτσι, ενώ η ΜΟΡ παραμένει μέθοδος εκλογής, αν και χρο­νο­βόρα, εν τούτοις η MGIT παρουσιάζει μεγάλη ευαισθησία και είναι τα­χύ­τερη. Η εφαρμογή νέων αξιόπιστων τεχνικών μειώνει εντυπωσιακά το χρό­­νο έκδοσης αποτελεσμάτων όσον αφορά τις λοιμώξεις από Mycobacterium spp., την ταυτοποίηση και τον έλεγχο αντοχής στα αντιφυ­μα­τικά φάρμακα έτσι ώστε η πρόγνωση της νόσου όσον αφορά την εργα­στη­ριακή διάγνωση της φυμα­τίω­σης και την παρακολούθηση της θεραπείας βελτιώνεται σημαντικά. / Re-emergence of tuberculosis in combination with the appearance of multidrug-resistant strains in recent yearsintensifies the need for application of rapid methods for the identification of mycobacteria. Even though staining for acid-fast bacilli (AFB) to identify Mycobacterium tuberculosis complex (MTB) is usually performed in the first 24 h of specimen receipt, it is considered a method of low sensitivity. Although time consuming, the standard detection method remains the culture of specimens with optimum results obtained after application of both solid and liquid media.The use of nucleic acid amplification techniques provides a sensitive and specific approach for the identification of MTB directly in clinical specimens. The Cobas Amplicor polymerase chain reaction for MTB (CA PCR, Roche Diagnostic Systems, Inc., Branchburg, N.J., USA) is a system that combines specimen processing with automated amplification and detection, easily adopted by a clinical laboratory. In the present study, the sensitivity, specificity, positive and negative predictive values of CA PCR and culture results of AFB-positive and AFB-negative respiratory specimens obtained by different means (expectoration, bronchoscopy, expectoration after broncho­scopy, lavages and aspirations), as well as in samples from normally sterile body fluids, were evaluated. A total of 3414 specimens from 2365 patients (1 to 3 specimens/patient) with clinical suspicion of tuberculosis were processed during the study period (1999-2003) by the Microbiology Laboratory at the University Hospital of Patras. The respiratory specimens consisted of 684 sputa, 1473 bronchoalveolar lavages (BAL), 625 sputa expectorated after bronchoscopy (SAB), 296 tracheal aspirations (TA) and 189 pleural fluids. Furthermore,23 gastric aspirates and 124 samples ofsynovial, pericar­dial, peritoneal and cerebrospinal fluids (CSF) were also examined in the present study. All specimens were processed according to conventional procedures for identification of mycobacteria; cultures were performed by inoculation of sediments directly on Löwenstein-Jensen slants (L-J, bioMerieux, SA Lyon, France) and in BACTEC MYCO/F-Sputa and BACTEC MYCO/F LYTIC culture vials (Becton Dickinson). Statistical analysis was conducted using the SPSS v.12.0 software package for Windows (SPSS Inc.). Comparison of Z-N and PCR results were expressed by means of percent agreement and Kappa statistic. Highest sensitivity of CA PCR was observed among all positive AFB samples, whereas sputa collected after bronchoscopy were the most appropriate specimens, showing 70% sensitivity and 98.6% specificity, among the AFB-negative samples. The increase of M. tuberculosis infections is a global health problem in terms of both the disease and resistance to commonly used drugs. For the reason of continuing develop­ment of resistance and especially multidrug-resistance of M. tuberculosis (MDR), Microbiology Laboratories should provide reliable antibiotic suscep­tibility testing results in the minimum of time. In the present study, antimy­co­bacterial drug susceptibility testing (AST) was performed on 88 non-replicate M. tuberculosis clinical isolates, using the Mycobacterium Growth Indicator Tube (MGIT) System and Etest as compared to the method of proportion (MOP), in order to evaluate the potential application of these manual methods in the routine diagnostic laboratory. Obtained results among four antituberculous agents, isoniazid (INH), rifampin (RIF), ethambutol (EMB) and streptomycin (STR) were compared. Isolates were recovered from different patients and were identified at species level by PCR and hybridization. Resistance to INH was detected in 20.5%, 29.5% and 12.5% of the isolates, followed by STR resistance (19.3% 26.1% and 1.1%), RIF (9.1%, 4.5% and 5.7%) and EMB (2.3%, 11.4% and 2.3%) as showed by the MOP, MGIT and Etest, respe­ctively. Sensitivity of the manual MGIT ranged from 37.5% for RIF resistance to 100% for EMB, while sensitivity of Etest ranged from 5.9% for STR to 62.5% for RIF. In conclusion, whilesputum samples and BAL are the preferable clinical specimens for MTB recovery, sputa expectorated after bronchoscop are those showing the highest sensitivity by PCR, both among Z-N-positive and negative specimens. The combination of Z-N and CA PCR including internal control of collected after bronchoscopy from a patient with clinical signs of infectionundoubtedly contribute to the early diagnosis of tuberculosis. According to our data, the sensitivity of the manual MGIT is higher in testing resistant isolates compared to Etest, with the exception of rifampin. On the other hand, Etest shows higher specificity as well as higher positive predictive values and it may be used for testing rifampin resistance. However, for a routine Clinical Microbiology Laboratory, among the manual methods tested, the method of proportion remains the “gold standard” even though a longer incubation period is needed.

Thesis (M.Cur) --University of Limpopo, 2011 / The aim of this study was to determine the factors that contribute to the increase in the number of tuberculosis (TB) patients in Mpumalanga Province, and to develop guidelines and recommendations to address the challenges of this health issue. The design of the study was qualitative phenomenological. The population consisted of all TB patients who were receiving treatment either at the intensive or the continuation phase. The sampling method was purposive and the sample size comprised 20 participants, of whom 10 were drawn from Shatale clinic at Bushbuckridge, and 10 from Mashishing clinic at Thabachweu municipalities in the Ehlanzeni district of Mpumalanga Province. The data was gathered by means of semi-structured interviews. Data analysis was performed, from which themes and categories were derived. This study revealed several factors that contributed to the increase in the number of TB patients at the study sites. The factors considered most important in this study were the general lack of knowledge of TB among participants, despite their various levels of education, poverty, overcrowding, poor ventilation in the shacks and Reconstruction and Development Program (RDP) houses, unemployment, lack of support while taking treatment, religious and ritual beliefs, and the influence of traditional healers who dispense herbal medicines with the dictum that participants have been possessed by evil spirits and witches. The majority of patients developed TB as a secondary opportunistic infection because of their HIV-positive status, and lack of capacity to practice personal hygiene and proper infection control. Guidelines, strategies and recommendations were formulated to address these public health challenges in the context nursing education, research, administration and practice

Mycobacterium tuberculosis est responsable de 8,7 millions de nouveaux cas de tuberculose et de 1,4 millions de décès en 2011. L’émergence de souches résistantes aux deux antituberculeux majeurs, isoniazide et rifampicine, (MDR) et aux antibiotiques de seconde ligne (XDR), ainsi que la difficulté d’éradiquer les formes « dormantes » du bacille nécessitent la recherche de nouveaux antibiotiques. Les β-lactamines n’ont jamais été utilisées en thérapeutique car M. tuberculosis produit une β-lactamase à large spectre, BlaC. Cependant, l’association d’une β-lactamine appartenant à la classe des carbapénèmes, le méropénème, et d’un inhibiteur de β-lactamase, l’acide clavulanique, est active sur M. tuberculosis incluant des souches XDR. Notre objectif a été de caractériser les cibles des carbapénèmes qui sont atypiques chez M. tuberculosis, parce que le peptidoglycane de cette bactérie contient majoritairement (80%) des ponts interpeptidiques formés par une classe particulière de transpeptidases, les L,D-transpeptidases. Nous avons comparé les cinq L,D-transpeptidases de M. tuberculosis au niveau de leur activité in vitro dans la formation des ponts interpeptidiques du peptidoglycane et dans la réaction d’inactivation par les carbapénèmes. Nous avons ainsi pu montrer que les cinq L,D-transpeptidases sont fonctionnelles in vitro. LdtMt1, LdtMt2, LdtMt4 et LdtMt5 sont capables de former des ponts interpeptidiques du peptidoglycane reliant l’acide aminé en position 3 d’un substrat tétrapeptidique donneur à l’acide aminé en position 3 d’un substrat tétrapeptidique accepteur. Ces mêmes enzymes peuvent également utiliser la D-méthionine comme accepteur dans une réaction d’échange de la D-Ala4 du substrat tétrapeptidique. LdtMt1, LdtMt2, LdtMt3 et LdtMt4 forment un complexe covalent avec les carbapénèmes. La réaction d’inactivation des L,D-transpeptidases par les carbapénèmes se déroulent en deux étapes. Dans un premier temps, un intermédiaire covalent réversible est formé (constante catalytique k1) puis la deuxième étape aboutit à la formation de l’acylenzyme (constante catalytique k2). La détermination des constantes catalytiques d’inactivation k1 et k2 a révélé d’importantes différences entre les carbapénèmes. Excepté pour LdtMt1, l’imipénème inactive plus rapidement les L,D-transpeptidases que les autres carbapénèmes suggérant que des modifications de la chaine latérale pourraient être envisagées pour optimiser l’activité « anti-mycobactérienne » de cette classe de β-lactamines. Nous avons en parallèle initié l’étude de la régulation des L,D-transpeptidases dans différentes conditions de culture ce qui permettra à terme d’identifier les L,D-transpeptidases essentielles pour la croissance et la persistance de M. tuberculosis. Ce travail pourrait déboucher sur l’identification de cibles essentielles permettant l’éradication des formes dormantes de M. tuberculosis qui sont très difficile à traiter. / Mycobacterium tuberculosis is responsible for 8.7 million of new cases of tuberculosis (TB) and 1.4 million of deaths in 2011. The emergence of strains resistant to the two first-line anti-TB drugs, isoniazid and rifampicin, (MDR), to second line-drugs (XDR) and the difficult to kill dormant forms of the bacilli require the discovery of new anti-TB antibiotics. β-lactams are usually not considered for tuberculosis treatment since M. tuberculosis produces a broad-spectrum β-lactamase, BlaC. However, the combination of β-lactam belonging to the carbapenem class, meropenem, with β-lactamase inhibitor, clavulanate, is notably active on XDR strains. Our aim was to characterize the carbapenem targets, atypical in M. tuberculosis, since peptidoglycan of this bacteria contains a majority (80%) of cross-links formed by a special transpeptidase family, the L,D-transpeptidases. We have compared the five L,D-transpeptidases of M. tuberculosis for their in vitro activities with respect to peptidoglycan dimers formation and for inactivation reaction by carbapenems. Thus, we have showed that the five L,D-transpeptidases were functional in vitro. LdtMt1, LdtMt2, LdtMt4 et LdtMt5 were able to form peptidoglycan cross-links binding the third amino acid of a donor tetrapeptide substrate with the third amino acid of an acceptor tetrapeptide substrate. These enzymes were also able to use D-methionine as an acceptor in exchange reaction of D-Ala4 of the donor tetrapeptide substrate. LdtMt1, LdtMt2, LdtMt3 et LdtMt4 formed a covalent adduct with carbapenems. The inactivation reaction of L,D-transpeptidases by carbapenems proceed through two steps. In first, a reversible covalent adduct is formed (catalytic constant k1), followed by a second step leading to acylenzyme formation (catalytic constant k2). The determination of kinetic constants of inactivation k1 et k2 revealed important differences between carbapenems. Except for LdtMt1, Imipenem inactivates L,D-transpeptidases more rapidly than other carbapenems indicating that modification of the carbapenem side chain could be used to optimize their anti-mycobacterial activity. In parallel, we have started the study of the L,D-transpeptidases regulation in various culture conditions will allow identifying the L,D-transpeptidases essential for growth and persistence of M. tuberculosis. This work might lead to identification of essential targets allowing eradication of M. tuberculosis dormant forms, which are difficult to treat with conventional anti-TB drugs.

MSc (Chemistry) / Department of Chemistry / Identification of unique leads represents a significant challenge in drug discovery. This challenge is widely visible in neglected diseases such as tuberculosis, which is an infectious disease caused by bacillus Mycobacterium tuberculosis. The urgent need in search of new biological entities to fight back TB and drug resistant TB is a drive behind this project. Several specific synthetic protocols have been developed using 1,3,5-triazines due to the important biological properties which they display. The chemistry and an extensive spectrum of biological activities of s-triazines have been examined since several decades and this heterocyclic core has received emerging consensus. Hence, the aim of this project was to synthesize novel anti-TB drugs total with the usage of 1,3,5-triazine as a linker between known anti-TB drugs together with different types of amines. A total of 20 compounds were synthesized, 3 compounds were mono-substituted with an average yield of 75 %, 6 compounds were di-substituted with an average yield of 63 % and 11 compounds were tri-substituted with an average yield of 93 %. Out of 10 compounds which were analysed for biological activity 8 of which showed biological activity against M.smegmatis. Furthermore compound 26 which was hybridized with an amine and a known anti-TB drug inhibited better biological activity. In conclusion the influence of cyanuric chloride in combination with pyrrolidine and anti-TB drugs deserves further study. The newly synthesized compounds were characterized by IR, melting point, GC-MS, biological testing, 1H and 13C NMR. / NRF

Tuberculosis (TB) is an infectious and fatal disease that ranks as the second leading killer worldwide. It is caused by Mycobacterium tuberculosis (Mtb) which is an obligate intracellular parasite that colonizes the alveolar macrophages of the immune system. The major health concern associated with TB is its co-infection with HIV and the development of strains with multi-drug resistance. The elimination of TB has been hindered due to the lack of understanding of the survival strategies used by this pathogen. Thus, research towards discovering new effective antibacterial drugs is necessary and a group of Mtb kinase enzymes were targeted in this study because these enzymes are crucial for metabolism, pathogenesis and, hence, the survival of Mtb. Kinases are a group of structurally distinct and diverse proteins that catalyze the transfer of the phosphate group from high energy donor molecules such as ATP (or GTP) to a substrate. The phosphorylation of proteins modifies the activity of specific proteins which is subsequently used to control complex cellular processes within Mtb. The starting point of this research targeted eight specific Mtb kinases namely; Nucleoside diphosphokinase, Homoserine kinase, Acetate kinase, Glycerol kinase, Thiamine monophosphate kinase, Ribokinase, Aspartokinase and Shikimate kinase. The aim of this project was to subclone the gene sequences for these eight recombinant Mtb kinases and express them in Escherichia coli, to purify the proteins and determine their activity. In the effort to find new lead compounds, the final stage of this study focused on the basic screening of the TB kinases against an extract prepared from Pelargonium sidoides, a medicinal plant, to identify any inhibitory effects. Although this traditional medicinal plant has been broadly researched and extensively used to treat TB, there is still a lack of understanding of this plant’s scientific curative effect. Various molecular and biochemical methods were used to achieve the aims of this project. The putative gene sequence was obtained from the annotated genome of H37Rv, deposited at NCBI as NC_000962.2. The genes encoding the kinases were successfully PCR-amplified from genomic DNA, cloned into an expression vector in-frame with a C- or N-terminal 6-histidine-tag and expressed in E. coli BL21 (DE3). The purification of the protein was complex, but various different methods and techniques were explored to obtain sufficient amounts of protein. The functional characterization of the kinases involved an HPLC enzyme assay that showed that the recombinant kinases were active. These enzymes were then screened against the potential inhibitory compounds in P. sidoides using enzyme assays to generate dose-response curves. This allowed an effective comparison not only of the Mtb kinases’ activity under normal conditions but also the kinases’ activity in the presence of a potential inhibitor. Overall, the inhibition of the enzymes required the presence of higher concentrations of the P. sidoides extract. However, the SK enzyme results presented a significantly higher inhibition and the lowest IC50 value, in comparison to the other kinases, which makes this kinase an attractive potential drug target against TB. In summation, cloning and purification of SK was successful, resulting in a concentration of 2030 μg/ml of purified enzyme and its activity analysis demonstrated enzyme functionality. This activity was reduced to zero in the presence of 1 x 102 mg/ml dilution of P. sidoides plant extract. This research conducted has extended the quality of information available in this field of study. These interesting results, proposing and identifying SK as a suitable potential target can be a starting point to significantly contribute and progress in this field of research, with the eventual goal of developing a drug to combat this fatal disease. / Life Sciences / M. Sc. (Life Sciences)

Tuberculosis (TB) is an infectious and fatal disease that ranks as the second leading killer worldwide. It is caused by Mycobacterium tuberculosis (Mtb) which is an obligate intracellular parasite that colonizes the alveolar macrophages of the immune system. The major health concern associated with TB is its co-infection with HIV and the development of strains with multi-drug resistance. The elimination of TB has been hindered due to the lack of understanding of the survival strategies used by this pathogen. Thus, research towards discovering new effective antibacterial drugs is necessary and a group of Mtb kinase enzymes were targeted in this study because these enzymes are crucial for metabolism, pathogenesis and, hence, the survival of Mtb. Kinases are a group of structurally distinct and diverse proteins that catalyze the transfer of the phosphate group from high energy donor molecules such as ATP (or GTP) to a substrate. The phosphorylation of proteins modifies the activity of specific proteins which is subsequently used to control complex cellular processes within Mtb. The starting point of this research targeted eight specific Mtb kinases namely; Nucleoside diphosphokinase, Homoserine kinase, Acetate kinase, Glycerol kinase, Thiamine monophosphate kinase, Ribokinase, Aspartokinase and Shikimate kinase. The aim of this project was to subclone the gene sequences for these eight recombinant Mtb kinases and express them in Escherichia coli, to purify the proteins and determine their activity. In the effort to find new lead compounds, the final stage of this study focused on the basic screening of the TB kinases against an extract prepared from Pelargonium sidoides, a medicinal plant, to identify any inhibitory effects. Although this traditional medicinal plant has been broadly researched and extensively used to treat TB, there is still a lack of understanding of this plant’s scientific curative effect. Various molecular and biochemical methods were used to achieve the aims of this project. The putative gene sequence was obtained from the annotated genome of H37Rv, deposited at NCBI as NC_000962.2. The genes encoding the kinases were successfully PCR-amplified from genomic DNA, cloned into an expression vector in-frame with a C- or N-terminal 6-histidine-tag and expressed in E. coli BL21 (DE3). The purification of the protein was complex, but various different methods and techniques were explored to obtain sufficient amounts of protein. The functional characterization of the kinases involved an HPLC enzyme assay that showed that the recombinant kinases were active. These enzymes were then screened against the potential inhibitory compounds in P. sidoides using enzyme assays to generate dose-response curves. This allowed an effective comparison not only of the Mtb kinases’ activity under normal conditions but also the kinases’ activity in the presence of a potential inhibitor. Overall, the inhibition of the enzymes required the presence of higher concentrations of the P. sidoides extract. However, the SK enzyme results presented a significantly higher inhibition and the lowest IC50 value, in comparison to the other kinases, which makes this kinase an attractive potential drug target against TB. In summation, cloning and purification of SK was successful, resulting in a concentration of 2030 μg/ml of purified enzyme and its activity analysis demonstrated enzyme functionality. This activity was reduced to zero in the presence of 1 x 102 mg/ml dilution of P. sidoides plant extract. This research conducted has extended the quality of information available in this field of study. These interesting results, proposing and identifying SK as a suitable potential target can be a starting point to significantly contribute and progress in this field of research, with the eventual goal of developing a drug to combat this fatal disease. / Life Sciences / M. Sc. (Life Sciences)