3. Electronic Theses and Dissertations (ETDs) - All submissions
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Item Detection and molecular epidemiology of ciprofloxacin-resistant Neisseria gonorrhoeae, using a real-time polymerase chain reaction (PCR)(2011-03-22) Magooa, Mahlape PreciousEmergence and spread of resistance to ciprofloxacin among Neisseria gonorrhoeae strains has reduced the options of effective treatment for gonococcal infections and has become a concern worldwide. Up until 2008, ciprofloxacin was recommended first-line therapy for treatment of presumptive N. gonorrhoeae infections in South Africa. At the time this MSc project was conceived, ciprofloxacin was still used as first-line therapy for presumptive gonococcal infections. A real-time polymerase chain reaction (PCR) assay was used to detect ciprofloxacin-resistant N. gonorrhoeae in DNA extracted from non-invasive urine samples collected as part of the national microbiological surveillance (NMS) programme during 2006-2007. The molecular epidemiology of ciprofloxacinresistant Neisseria gonorrhoeae was investigated by sequencing the quinolone resistance determining regions (QRDR) of the gyrA and parC genes of N. gonorrhoeae and performing N. gonorrhoeae multi-antigen sequence typing (NGMAST). As part of the NMS program for sexually transmitted infections (STIs) urine and urethral swabs were collected from men presenting with urethral discharge at primary health care clinics in Johannesburg (Gauteng), Cape Town (Western Cape) and Kimberley (Northern Cape). Urine samples and cultured N. gonorrhoeae isolates from 2006-2007 were stored at -700C and available for this study. Gonococci, previously isolated from urethral swabs, were subcultured directly onto New York City media. Isolate identity was re-confirmed by typical colony morphology and biochemical tests. Urine samples from Johannesburg were tested in order to develop the real-time PCR protocol. Subsequently, paired urethral swab DNA and N. gonorrhoeae cultures were tested from NMS patients recruited in Kimberley and Cape Town. Where possible, the PCR assay results were compared with paired antibiotic susceptibility data for ciprofloxacin. Quinolone resistance determining regions (QRDR) for gyrA and parC were screened for known point mutations associated with resistance to ciprofloxacin. Detection of mutations by the real-time PCR assay generally agreed with the phenotype of either decreased susceptibility or resistance to ciprofloxacin. All ciprofloxacin resistant gonococcal isolates had the same gyrA and parC mutations, which initially suggested that quinolone resistant N. gonorrhoeae (QRNG) in Kimberley, Cape Town and Johannesburg, may be attributed to the spread of a single clone. The use of a more discriminatory typing scheme, Neisseria gonorrhoeae Multi-Antigen Sequence Typing (NG-MAST) genotyping, revealed that ciprofloxacin resistant gonococcal isolates in Johannesburg and Cape Town were heterogeneous, with sequence type (ST) 217 being most prevalent in both cities (5/16, Johannesburg; 7/11, Cape Town). In contrast, all eight QRNG isolates from Kimberley were typed as ST 533. The use of molecular methods allowed ciprofloxacin antimicrobial susceptibility determination by PCR in non-invasive specimens. This is useful in situations where bacterial cultures are unavailable or die before antimicrobial susceptibility testing can be performed. Molecular assays to detect ciprofloxacin resistance may guide physicians as to the most ideal antimicrobial combinations for individual patient treatment. As a result of emerging widespread resistance gonococci to ciprofloxacin, in 2008, the Department of Health recommended that ciprofloxacin be removed as a first line therapy in the South African national sexually transmitted infections treatment guidelines for treatment of urethritis, cervicitis and their complications. Although ciprofloxacin is no longer used as a first-line therapy to treat gonorrhoea within our country, it may still be used in cases of severe penicillin allergy or as part of multi-drug therapy for gonococcal infections in the future. The ability to detect ciprofloxacin resistance by real-time PCR will be a useful technique in such situations.Item An evaluation of a chronic disease outreach program (CDOP) - a primary care and tertiary care kidney and cardiovascular prevention, detection and management program(2011-02-01) Katz, Ivor JonathanBackground: Chronic diseases have increased worldwide. Despite the significant advances in medical science, the management of chronic diseases continues to be poor. To meet this challenge, we need to try to implement existing chronic illness models of prevention, early detection, and risk factor management. This is achievable in part by linking primary health care clinicians, such as primary health care nurses (PHCNs) and hospital-based medical specialists. This study evaluated a ‘real life’ chronic disease outreach program (CDOP), which assisted PHCNs with the early detection and management of chronic illnesses known to cause chronic kidney disease (CKD) and cardiovascular disease (CVD). PHCNs are critical in the management of chronic illnesses but they require ongoing support of and links with specialists. This will ensure that current guidelines reach the people receiving primary health care (PHC) and detection of those needing referrals. Aims: The study aimed to determine if CDOP was an effective method for the early detection and management of diabetic and hypertensive patients at high risk for complications like stroke, ischaemic heart disease and CKD. It also aimed to evaluate the PHCNs’ knowledge and motivation, and to elucidate the challenges facing the current health system in the management of patients with chronic conditions. Methods: Patients at risk for complications were enrolled for increased monitoring and clinical support and management, at 20 clinics in Soweto, South Africa (SA). CDOP used a paper-based support and patient care system, modelled on the Wagner Chronic Illness Care Model (CICM). The components for evaluation included: (i) Focus on monitoring functional and clinical outcomes (ii) Health system interventions, such as increased ‘decision support’ and the development of a ‘prepared motivated health care team’ and (iii) Enhancing PHCNs’ knowledge and motivation. The evaluation followed the various elements of the Wagner CICM, as well as drawing on the WHO Innovative Care for Chronic Conditions (ICCC) Framework. A cohort analysis of functional and clinical outcomes in enrolled patients was conducted. PHCN knowledge and motivation was assessed through self administered questionnaires. Health worker knowledge was evaluated through the use of case scenarios and multiple choice questions. On the theme of health worker motivation, Franco’s model, with Penn-Kekana’s adaptation, was used to develop the questions and analyse diary recordings. Diary recordings of PHCNs and meetings with regional and provincial health managers’ discussions were collected by CDOP staff during follow-up focus groups and feedback meetings. Diaries were analysed thematically. The CDOP evaluation is thus a triangulated analysis of clinical and functional outcomes, diary recordings, and the self-administered questionnaire. Results: The CDOP ran from 2003-2006, during which time 618 patients (61% females, 39% males) deemed at risk of CKD or CVD were enrolled; 55% had uncontrolled hypertension (HTN), 45% DM with HT and/or proteinuria. Patients were followed for 2 years. In total, 108 patients completed 2 years of follow up, most of whom were referred for specialist support (n=69, 11%), more intensive medication regimes or because were not available in the PHC system. Most did not require referral (515, 82%), 35 (6%) were referred but never arrived at the hospital and 6 (1%) died. Twelve percent had advanced CKD, 2% required dialysis, 6.9% required medications not available to primary care clinics, and 1% died. As a tool to detect those needing referral, the program was successful. The sensitivity and specificity for detecting those needing referral was 95% and 100%, respectively.. However, although PHCNs were able to detect high risk patients, not all those referred arrived at the hospital. Hypertension, blood glucose, cholesterol and proteinuria control significantly improved in those followed (p<0.01) over 2 years, but no improvement was noted with weight control. Importantly, proteinuria and kidney function, in patients with static stable renal function, measured by estimated GFR equations and urine dipstick or albumin creatinine ratio (ACR), did not worsen significantly. Of the remaining 510 patient enrolled but not followed up, 213 (35%) were reabsorbed into the routine clinics, and a further, 123 (20%) of patients enrolled were lost to follow up completely. The diary recording thematic analysis revealed the problem of poor patient follow up, attributed to the poor existing health system in the clinics, competing demands on PHCNs, staff shortages, high staff turnover, and the low motivation and morale of clinicians. The analysis of the health worker questionnaire showed improved motivation and statistically better knowledge in those PHCNs involved with CDOP compared to those who were not exposed to the program (p<0.0034). Conclusions: CDOP was successful in supporting PHCNs, detecting patients with advanced disease and ensuring their early referral. Such programs are able to correctly detect people with disease, but this is dependent on the health and program systems being intact. It also improved patient risk factor control in the sub-set of referred patients and impacted on PHCNs’ existing knowledge and motivation for caring for patients. Its weaknesses were related to the poor existing health systems and infrastructure, and the poor integration of chronic illness care in the region. The PHC clinics had poor follow up compared with that in the hospital setting. The study also revealed an overworked, poorly supported, and frustrated primary health care team. This was despite the fact that the PHCNs were willing and motivated to deliver a good service.