Würzburg, Univ., Diss., 2009. / Zsfassung in dt. Sprache.

Zugl.: Aachen, Techn. Hochsch., Diss., 2009

abstract: In sub-Saharan Africa, an invasive form of nontyphoidal Salmonella (iNTS) belonging to sequence type (ST)313 has emerged as a major public health concern causing widespread bacteremia and mortality in children with malaria and adults with HIV. Clinically, ST313 pathovars are characterized by the absence of gastroenteritis, which is commonly found in “classical” nontyphoidal Salmonella (NTS), along with multidrug resistance, pseudogene formation, and chromosome degradation. There is an urgent need to understand the biological and physical factors that regulate the disease causing properties of ST313 strains. Previous studies from our lab using dynamic Rotating Wall Vessel (RWV) bioreactor technology and “classical” NTS strain χ3339 showed that physiological fluid shear regulates gene expression, stress responses and virulence in unexpected ways that are not observed using conventional shake and static flask conditions, and in a very different manner as compared to ST313 strain D23580. Leveraging from these findings, the current study was the first to report the effect of fluid shear on the pathogenesis-related stress responses of S. Typhimurium ST313 strain A130, which evolved earlier than D23580 within the ST313 clade. A130 displayed enhanced resistance to acid, oxidative and bile stresses when cultured in the high fluid shear (HFS) control condition relative to the low fluid shear (LFS) condition in stationary phase using Lennox Broth (LB) as the culture medium. The greatest magnitude of the survival benefit conferred by high fluid shear was observed in response to oxidative and acid stresses. No differences were observed for thermal and osmotic stresses. Based on previous findings from our laboratory, we also assessed how the addition of phosphate or magnesium ions to the culture medium altered the acid or oxidative stress responses of A130 grown in the RWV. Addition of either phosphate or magnesium to the culture medium abrogated the fluid shear-related differences observed for A130 in LB medium for the acid or oxidative stress responses, respectively. Collectively, these findings indicate that like other Salmonella strains assessed thus far by our team, A130 responds to differences in physiological fluid shear, and that ion concentrations can modulate those responses. / Dissertation/Thesis / Masters Thesis Microbiology 2017

Made available in DSpace on 2014-06-11T19:24:45Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-10-02Bitstream added on 2014-06-13T19:31:45Z : No. of bitstreams: 1 cruz_ar_me_botfmvz.pdf: 295083 bytes, checksum: ab5cfdefcaea9966bbd7d2f696f50b96 (MD5) / Universidade Estadual Paulista (UNESP) / A passagem de bactérias resistentes dos animais ao homem é possível. As amostras foram coletadas de cães, machos e fêmeas, de diferentes raças e idade, com infecções bacterianas variadas. Foram realizados cultura e antibiograma das bactérias isoladas (n=100), sendo avaliadas como sensíveis ou resistentes. Grupo das bactérias Gram-negativas: tetraciclina 83,02%, azitromicina 81,48%, doxiciclina 77,78%, ampicilina 62,96%, ceftiofur e florfenicol 50%, cefalexina 46,3%, enrofloxacino 44,44%, norfloxacino 18,52%, gentamicina 20,37%, levofloxacino 27,78%, amoxicilina + ácido clavulânico 31,48%, ciprofloxacino 31,48%, amicacina e ceftriaxona 33,33%, cloranfenicol e sulfa + trimetoprin 35,19%. Grupo dos Streptococcus: tetraciclina 80%, eritromicina 72%, enrofloxacino e levofloxacino 52%, ampicilina, azitromicina, ciprofloxacino, norfloxacino, penicilina G e sulfa + trimetoprin 48%, amoxicilina + ácido clavulânico 4%, cefalexina 12%, florfenicol 24%, ceftiofur, ceftriaxona e oxacilina 28%, cloranfenicol 32%. Grupo dos Staphylococcus spp: ampicilina 57,14%, sulfa + trimetoprin e tetraciclina 52,38%, amicacina, amoxicilina + ácido clavulânico, gentamicina, levofloxacino, 4,76%; cefalexina, ceftiofur, ceftriaxona e cloranfenicol, 9,52%; vancomicina 13,33%, norfloxacino 19,05%; ciprofloxacino, enrofloxacino e oxacilina 23,81% e azitromicina 33,33%. Os cães são reservatórios de bactérias multidrogas resistentes que podem transmitir por meio de plasmídios os genes de resistência, explicando a resistência de bactérias isoladas de cães à antimicrobianos de uso humano como a vancomicina. / The transmission of resistant bacteria from animals to humans is possible. Samples were collected from different breeds of dogs in different ages including males and females, with a variety of bacterial infections. The culture and antibiograma of isolated bacteria were analysed (n = 100), being evaluated as sensitive or resistant. Group of Gram-negative bacteria tetracycline 83.02%, azithromycin 81.48%, doxycycline 77.78%, ampicillin 62.96%, ceftiofur and florfenicol 50%, cephalexin 46,3%, enrofloxacin 44.44%, norfloxacin 18.52%, gentamicin 20.37%, levofloxacin 27.78%, amoxicillin + clavulanic acid 31.48%, ciprofloxacin 31.48%, amikacin and ceftriaxone 33.33%, chloramphenicol and trimethoprim + sulfa (35.19%). Streptococcus’ group: tetracycline 80%, erythromycin 72%, enrofloxacin and levofloxacin 52%, ampicillin, azithromycin, ciprofloxacin, norfloxacin, penicillin G and sulfamethoxazole + trimethoprim 48%, amoxicillin + clavulanic acid 4%, cephalexin 12%, florfenicol 24%, ceftiofur, ceftriaxone, and oxacillin 28%, chloramphenicol 32%. Group of Staphylococcus spp: ampicillin 57.14%, sulfamethoxazole + trimethoprim and tetracycline 52.38%, amikacin, amoxicillin + clavulanic acid, gentamicin, levofloxacin, 4.76%, cephalexin, ceftiofur, ceftriaxone, and chloramphenicol 9.52%, vancomycin 13.33%, norfloxacin 19.05% ciprofloxacin, enrofloxacin and oxacillin 23.81% and azithromycin 33.33%. Dogs have resistant-multidrug bacteria that might pass through the plasmid resistant genes, explaining the resistance of isolated bacteria from dogs to human use of antimicrobials such as vancomycin.

The Tuberculosis infection rate has been generally escalating due to poor health conditions in the Gweru district of Zimbabwe. The study therefore seeks to identify the risk factors that affect TB treatment in the Gweru district. A cross sectional study was carried out in which a questionnaire was employed for data collection on 113 respondents. A binary logistic regression model was employed for data analysis. A total of 98 TB patients were interviewed: [50 respondents (44.0%) had Multi-drug resistant Tuberculosis and 63 respondents (56.0%) had general Tuberculosis). Before being enrolled into the study, an informed consent form was given to each of the participants. The data was then put into excel and later transferred to SPSS for analysis. Out of the 14 potential risk factors of TB treatment, only 6 variables (side effects, gender, alcohol use, HIV status, smoking during the treatment period and having been pre-exposed to TB drugs) were statistically significant in their association with treatment failure.

京都大学 / 0048 / 新制・論文博士 / 博士(人間健康科学) / 乙第13006号 / 論人健博第1号 / 新制||人健||3(附属図書館) / 32934 / (主査)教授 藤井 康友, 教授 澤本 伸克, 教授 一山 智 / 学位規則第4条第2項該当 / Doctor of Human Health Sciences / Kyoto University / DFAM

No description available.

Background: Multidrug-resistant tuberculosis (MDR-TB) patients receive aminoglycosides as part of their treatment. These drugs are ototoxic, and can cause permanent damage to the cochlea, resulting in a debilitating hearing loss, which has a negative impact on an individual's quality of life. Early detection and management of an ototoxic hearing loss can minimise the impact of the hearing loss on the person's social, emotional, and vocational wellbeing. While patients with MDR-TB are often very ill, it might be ideal to use an objective test that does not require active participation from the patient. In this way, the reliability and validity of the test will not be affected by the patient's state. Distortion product otoacoustic emissions (DPOAEs) at 2f1-f2 are a viable option, as it evaluates cochlear function, specifically the outer hair cells, which are affected first by ototoxic medication. Method: This thesis used a sequential study design aimed to determine the DPOAE stimulus parameters that yield (a) the highest level and the most reliable, sensitive and specific DPOAEs reported in the literature, (b) the highest level and the most reliable DPOAEs in healthy, normally hearing adults, and (c) the most sensitive and specific DPOAEs in participants with MDR-TB patients receiving ototoxic medication. High frequency pure tone audiometry (defined in this thesis as frequencies > 8 kHz) was used as the gold standard. Descriptive statistics, the intraclass correlation coefficient, Pearson's correlation coefficient and mixed model analyses were used to analyse the data. Results: Systematic review: The results of the systematic review indicated an L1/L2 setting of 75/75 dB SPL and f2/f1 value from 1.20 to 1.22 yielded the highest level DPOAEs. The systematic review results for stimulus parameters that yielded the highest test-retest reliability, sensitivity and specificity were inconclusive. Preliminary study with healthy normal hearing participants: The results of the preliminary study in healthy, normal-hearing participants indicated that the highest levels of DPOAEs were elicited with L1/L2 intensity levels of 65/65 and 65/55 dB SPL, and f2/f1 ratios of 1.18, 1.20 and 1.22, as determined by mixed model analyses (p < 0.05). These same stimulus parameters yielded the most reliable DPOAEs in both ears, as determined by intraclass correlation coefficient analysis. Main study with healthy, normal-hearing participants: Descriptive statistics and mixed model analysis showed stimulus intensity levels L1/L2 of 65/55 dB SPL, and f2/f1 ratios of 1.18 and 1.20, elicited the largest DPOAEs. The ratio of 1.20 yielded the largest DPOAEs < 5000 Hz and f2/f1 ratio of 1.18 the largest DPOAEs ≥ 5000 Hz. The second highest DPOAE levels were elicit by L1/L2 = 65/65 dB SPL and f2/f1 = 1.18. The test-retest reliability in this sample was not influenced by changing the stimulus parameters, and DPOAEs were only unreliable at an f2 frequency of 8 000 Hz. Study in participants with MDR-TB: Results in participants with MDR-TB receiving ototoxic medication indicated that the highest levels of DPOAEs were elicited with L1/L2 = 65/55 and an f2/f1 ratio of 1.18 at f2 ≥ 5000 Hz, followed by 65/65 and 1.18. For f2 < 5000 Hz, stimulus intensities of L1/L2 = 65/55 and an f2/f1 ratio of 1.20 yielded the largest DPOAE levels. Relating to sensitivity and specificity, the stimulus parameter combination of 65/55 dB and 1.18 detected the highest number of ears with outer hair cell damage in participants with MDR-TB receiving ototoxic medication. Conclusion: It should be considered to use an f2/f1 ratio of 1.18 for f2 ≥ 5000 Hz and 1.20 for f2 < 5000 Hz when monitoring for ototoxicity, to assist with early identification of outer hair cell damage, in conjunction with high frequency pure tone audiometry. This finding needs to be confirmed in a larger sample of participants with MDR-TB receiving ototoxic medication.

Thesis (MScMedSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Central dogma suggests that mutations in target genes is the primary cause of resistance to first and second-line anti-TB drugs in Mycobacterium tuberculosis. However, it was previously reported that approximately 5% of Rifampicin mono-resistant clinical M. tuberculosis did not harbor mutations in the rpoB gene. The present study hypothesized that active efflux plays a contributory role in the level of intrinsic resistance to different anti-TB drugs (Isoniazid, Ethionamide, Pyrazinamide, Ethambutol, Ofloxacin, Moxifloxacin, Ciprofloxacin, Streptomycin, Amikacin and Capreomycin in RIF mono-resistant clinical M. tuberculosis isolates with a rpoB531 (Ser-Leu) mutation. This study aimed to define the role of Efflux pump inhibitors (verapamil, carbonylcyanide m-chlorophenylhydrazone and reserpine) in enhancing the susceptibility to different anti-TB drugs in the RIF mono-resistant clinical isolates. The isolates were characterized by determining the level of intrinsic resistance to structurally related/unrelated anti-TB drugs; determining the effect of EPIs on the level of intrinsic resistance in the isolates and comparing the synergistic properties of the combination of EPIs and anti-TB drugs. To achieve this, genetic characterization was done by PCR and DNA sequencing. Phenotyping was done by the MGIT 960 system EpiCenter software to determine the MICs of the different anti-TB drugs and the effect of verapamil and carbonylcyanide m-chlorophenylhydrazone on determined MICs. Due to inability to test reserpine in a MGIT, a different technique (broth microdilution) was used for the reserpine experiment. Additionally; fractional inhibitory concentrations (FIC) indices were calculated for each of these drugs. The FIC assess the anti-TB drugs/inhibitor interactions. STATISTICA Software: version 11 was used for statistical analysis. Results revealed that the RIF mono-resistant isolates were sensitive at the critical concentrations of all 10 drugs tested, with the exception of Pyrazinamide. This could be explained by the technical challenges of phenotypic Pyrazinamide testing. A significant growth inhibitory effect was observed between the combination of EPI and anti-TB drug exposure in vitro. This suggests that verapamil, carbonylcyanide m-chlorophenylhydrazone and reserpine play a significant role in restoring the susceptibility (decrease in intrinsic resistance level) of the RIF mono-resistant isolates to all anti-TB drugs under investigation. Additionally, a synergistic effect was observed by the combination treatment of the anti-TB drugs with the different EPIs. Based on these findings, we proposed a model suggesting that efflux pumps are activated by the presence of anti-TB drugs. The activated pumps extrude multiple or specific anti-TB drugs out of the cell, this in turn decrease the intracellular drug concentration, thereby causing resistance to various anti-TB drugs. In contrast, the addition of EPIs inhibits efflux pump activity, leading to an increase in the intracellular drug concentration and ultimate cell death. This is the first study to investigate the effect of different efflux pumps inhibitors on the level of intrinsic resistance to a broad spectrum of anti-TB drugs in drug resistant M. tuberculosis clinical isolates from different genetic backgrounds. The findings are of clinical significance as the combination of treatment with EPI and anti-TB drugs or use of EPIs as adjunctives could improve MDR-TB therapy outcome. / AFRIKAANSE OPSOMMING: Sentrale dogma beweer dat mutasies in teiken gene die primêre oorsaak van die weerstandheid teen anti-TB-middels in Mycobacterium tuberculosis is. Vorige studies het getoon dat ongeveer 5% van Rifampisien enkelweerstandige kliniese M. tuberculosis isolate nie ‘n mutasie in die rpoB geen het nie. Die hipotese van die huidige studie was dat aktiewe pompe 'n bydraende rol speel in die vlak van intrinsieke weerstandheid teen 10 verskillende anti-TB-middels (Isoniasied, Ethionamied, Pyrazinamied, Ethambutol, Ofloxacin, Moxifloxacin, Siprofloksasien, Streptomisien, Amikasien and Capreomycin) in RIF enkelweerstandige kliniese M . tuberculosis isolate met 'n rpoB531 (Ser-Leu) mutasie. Die doel van hierdie studie was om die rol van uitpomp inhibeerders (verapamil, carbonylcyanide m-chlorophenylhydrazone en reserpien) te definieer in die verbetering van die werking vir verskillende anti-TB-middels in die RIF enkelweerstandige kliniese isolate. Die doelstellings van die studie was om die vlak van intrinsieke weerstandigheid teen struktureel verwante/onverwante anti-tuberkulose middels asook die effek van die EPIs op die vlak van intrinsieke weerstand in die isolate is bepaal. Verder is sinergistiese eienskappe van die kombinasie van EPIs en anti-TB-middels ondersoek. Hierdie doelstellings is bereik deur genetiese karakterisering deur PKR en DNS volgorde bepaling. Fenotipering is gedoen deur gebruik te maak van MGIT 960 EpiCenter sagteware om die Minimum Inhibisie Konsentrasie (MIC) van die verskillende anti-TB-middels en die effek van verapamil en carbonylcyanide m-chlorophenylhydrazone op die MIC te bepaal. Reserpien kan nie in die MGIT sisteem getoets word nie, and daarom is 'n ander tegniek (mikro-verdunning) is gebruik om die effek van reserpien te toets. Fraksionele inhiberende konsentrasies (FIC) is bereken vir elk van hierdie middels die anti-TB-middels / inhibeerder interaksies te bepaal. STATISTICA v11 sagteware is gebruik vir alle statistiese analises. Resultate van hierdie studie toon dat die RIF enkelweerstandige isolate sensitief is teen kritieke konsentrasies van al die middels, met die uitsondering van Pyrazinamied. Weerstandigheid van Pyrazinamied kan wees as gevolg van welbekende tegniese probleme met die standaard fenotipiese pyrazinamied toets. ‘n Beduidende groei inhiberende effek is waargeneem tussen die kombinasie van EPI en anti-TB middel blootstelling in vitro. Dit dui daarop dat verapamil, CCCP en reserpine 'n belangrike rol speel in die herstel van die sensitiwiteit (afname in intrinsieke weerstand vlak) van die RIF enkelweerstandige isolate aan alle anti-TB-middels wat ondersoek is. Daarbenewens is 'n sinergistiese effek waargeneem deur die kombinasie van die verskillende anti-TB-middels en die verskillende EPIs. Op grond van hierdie bevindinge het ons ‘n model voorgestel wat toon dat uitvloei pompe geaktiveer word deur die teenwoordigheid van anti-TB-middels en die geaktiveerde pompe dan verskeie of spesifieke anti-TB-middels uit die sel pomp. Dus verminder die intrasellulêre konsentrasie van die middel en veroorsaak daardeur weerstandigheid teen verskeie anti-TB-middels. Die byvoeging van EPIs inhibeer uitvloei pompe se werking en lei tot 'n toename in die intrasellulêre konsentrasie van die middels en uiteindelik die dood van die selle. Hierdie is die eerste studie wat die effek van verskillende uitvloei pompe inhibeerders op die vlak van intrinsieke weerstand teen 'n breë spektrum van anti-TB-middels in die middel-weerstandige kliniese isolate ondersoek. Die bevindinge kan van belangrike kliniese belang wees aangesien die kombinasie van behandeling met EPI en anti-TB-middels die uitkoms MDR-TB terapie kan verbeter.

結核病仍是全球疾病和死亡的主要原因。雖然人均新發結核病例自2003年以來一直下降，耐多藥（MDR）和廣泛耐藥（XDR）的結核病例的突然增加為全球疾病控制帶來了新的威脅。結核分枝杆菌（MTB）北京株在過去十年越来越受重視，皆因其席捲亞洲，前蘇聯，和包括美國在內的好幾個地方。北京株在動物實驗中也表現出高毒性和耐多藥的傾向。目前結核菌廣泛耐藥定義為至少對異煙肼和利福平耐藥，再加上任何氟喹諾酮類，和至少一個二線藥物。我們對這種病菌的生物知識仍然有限。在這研究，我們為來自香港和福建五株MTB北京株進行了基因組測序，其中兩株的耐藥性遠超XDR標準 - “全耐藥“（TDR）的表型。五個北京株的比較基因組學為我們提供了在北京株的毒力相關基因的啟示。一個約4 KB大小的片段被找出来了，此片段是所有已知MTB中都没有的。我們討論了此片段對MTB進化的含義。當我們研究在北京耐藥株的獨特基因變化時發現，DNA修復和香葉醇降解有關連。我們還觀察到大的缺失（D）和截斷（T）的事件，顯著高於框移位（F）的突變。此外，在TDR菌株出現的FDT事件更頻繁地涉及到最佳生長和麻風分枝杆菌的基因組中保留的基因。這方面的証據表明，MTB通過缩减進化發展極端耐藥性。適應度的顯著降低也許解釋了TDR菌株的稀缺 。 / Tuberculosis (TB) remains one of the major causes of illness and death globally. Although the number of new TB cases per capita has been falling since 2003, the emergence of multidrug resistant (MDR) and extensively drug resistant (XDR) cases of TB poses new threat to the successful worldwide control of the disease (WHO, 2008; Iseman, 2007). The Beijing lineage of Mycobacterium tuberculosis (MTB) has received much attention over the past decade due to its prevalence throughout Asia, parts of the former Soviet Union, and several other geographical locations including the United States. The strain also demonstrated hypervirulence in animal models and an increased likelihood to develop multidrug resistance. The current definition of XDR in TB is defined as resistance to at least isoniazid and rifampicin, any fluoroquinolone, and with at least one of the three second-line drugs. Here we show that our knowledge of the biology of this pathogen is still limited. We performed genome sequencing and reported the complete genomes of five Beijing isolates from Hong Kong and Fujian, of which two were shown to have drug resistance that is far beyond the current XDR standard - a "Totally Drug Resistance" (TDR) phenotype. Comparative genomics of the five Beijing isolates provided us insights into the virulence-related genes in the Beijing family. A distinct region of about 4 kb in size that are absent in all known complete genomes of MTB was also identified. The evolutionary implications of this region were discussed. When we investigated the unique genetic changes in drug resistant Beijing strains, a correlation to DNA repair and geraniol degradation was implicated. We have also observed that the big deletions (D) and truncations (T) events were significant higher when compare with frameshift (F) mutations. Moreover, the FDT events in TDR strains were more frequently found in genes that are involved in growth attenuation and retained in the genome of the Mycobacterium leprae. This evidence suggests that MTB develops its extreme drug resistance through the reductive evolution. The significant decrease in the fitness may explain the rareness of TDR strains. / Detailed summary in vernacular field only. / Leung, Ka Kit. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 93-108). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese. / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Epidemiology - a ubiquitous threat --- p.1 / Chapter 1.2 --- Surviving the Hell --- p.3 / Chapter 1.3 --- Relatives of M. tuberculosis --- p.4 / Chapter 1.4 --- The age of M. tuberculosis --- p.5 / Chapter 1.5 --- Characteristics of Beijing strains --- p.6 / Chapter 1.6 --- Drug resistance --- p.7 / Chapter 1.7 --- Genome sequencing --- p.9 / Chapter 1.7.1 --- Conventional sequencing --- p.9 / Chapter 1.7.2 --- High-throughput sequencing --- p.10 / Chapter 1.8 --- Sequence assembly --- p.11 / Chapter 1.8.1 --- De novo assembly --- p.11 / Chapter 1.8.2 --- Reference mapping --- p.12 / Chapter Chapter 2 --- Materials and Methods --- p.14 / Chapter 2.1 --- Sample preparation --- p.14 / Chapter 2.2 --- DNA extraction and genome sequencing --- p.18 / Chapter 2.3 --- Gap filling and finishing --- p.20 / Chapter 2.3.1 --- In silico gap verification --- p.20 / Chapter 2.3.2 --- Comparison among different reference mapped contigs --- p.24 / Chapter 2.3.3 --- Experimental work --- p.26 / Chapter 2.4 --- Bioinformatics analysis --- p.27 / Chapter 2.4.1 --- Genome annotation --- p.27 / Chapter 2.4.2 --- Phylogeny analysis --- p.27 / Chapter 2.4.3 --- Variation analysis --- p.28 / Chapter 2.4.4 --- In silico functionality analyses --- p.29 / Chapter Chapter 3 --- Results --- p.30 / Chapter 3.1 --- Genome features of M. tuberculosis Beijing genotype strains --- p.30 / Chapter 3.2 --- Phylogeny of M. tuberculosis Beijing genotype strains --- p.36 / Chapter 3.3 --- Evolutionary implications of a 4kb-insertion in Beijing strains --- p.40 / Chapter 3.4 --- Beijing family specific gene variations --- p.48 / Chapter 3.5 --- Drug resistance --- p.52 / Chapter Chapter 4 --- Discussions --- p.75 / Chapter 4.1 --- 4kb insertion, a potential bridge to our knowledge gap --- p.75 / Chapter 4.2 --- Beijing common and Beijing drug resistant specific variations --- p.77 / Chapter 4.3 --- Regions of deletion --- p.79 / Chapter Chapter 5 --- Conclusions --- p.82 / Chapter Chapter 6 --- Future Work --- p.84 / Chapter 6.1 --- Compensatory mutation study --- p.84 / Chapter 6.1.1 --- Database construction for drug resistance compensatory mutations --- p.85 / Chapter 6.2 --- Non-protein coding region study --- p.92