Epidemiology of extended spectrum beta-lactamase and carbapenemase-producing bacteria in stool from apparently healthy children, South Africa

Background: The prevalence of extended-spectrum beta-lactamase (ESBL) - and carbapenemase-producing Enterobacteriaceae in healthy humans in the community is largely unknown. We aimed to determine the prevalence and genetic characteristics of ESBL- and carbapenemase-producing Enterobacteriaceae in stools from healthy infants and their mothers, and to determine the risk factors associated with their carriage. Methods: This study was nested within the Drakenstein Child Health Study, a birth cohort in a semi-rural region of Western Cape Province, South Africa. Maternal and infants faecal samples (including the meconium) were collected at birth and at two additional time-points (5-12 and 20-28 weeks) from the infants only. Samples were screened for ESBLs and carbapenemase-producing organisms using ChromID ESBL and ChromID CARBA media, respectively. Identification of suspect ESBL/carbapenemase-producing isolates and antibiotic susceptibility were determined using the Vitek 2 system. ESBL production was confirmed using the combination disc test, and that of carbapenemase using the modified hodge test. Selected ESBL and carbapenemase genes were evaluated by the singleplex conventional polymerase chain reaction and Sanger sequencing. Risk factors were assessed by univariate analysis using the EPI Info version 7 software

Nasopharyngeal colonization dynamics with Streptococcus pneumoniae and associated antimicrobial resistance in a South African birth cohort

Introduction: Nasopharyngeal (NP) colonization by Streptococcus pneumoniae (the pneumococcus) precedes the development of respiratory tract infection. Colonization by antimicrobial-resistant pneumococci, especially in infants, is a major public health concern as pneumococcus is a frequent cause of bacterial acute respiratory tract infections among children. This study longitudinally investigated antimicrobial resistance amongst pneumococci colonizing the nasopharynx of South African infants immunized with the 13- valent pneumococcal conjugate vaccine (PCV13). Furthermore, the study explored strainlevel pneumococcal colonization patterns and associated antimicrobial resistance determinants as well as the composition of the NP antibiotic resistome using shotgun metagenomic sequencing. Methods: NP swabs were collected every second week from birth through the first year of life from 137 infants who were immunized with 2+1 doses of PCV13. These were the first 137 infants enrolled in the cohort who had the most complete fortnightly NP sampling (defined as at least 23-26 fortnightly collected NP swabs). Pneumococci were identified and serotyped using conventional techniques, and their antibiotic susceptibility profiles determined by disc diffusion and E-test. A subset of 196 NP samples from 23 infants were selected based on changes in serotype or antimicrobial resistance. These were subjected to broth enrichment, total nucleic acid extraction and subsequent shotgun metagenomic sequencing. Sequence reads were assembled and aligned to reference pneumococcal genomes. In-silico pneumococcal capsular, multilocus sequence typing, and antimicrobial resistance determinants were described. Finally, antibiotic resistance genes were identified from all bacterial contigs, to determine the NP resistome. Results: 1520 pneumococcal (760 non-duplicate) isolates were recovered from 137 infants; including non-typeable (n = 99), PCV13 (n = 133), and non-PCV13 serotypes (n = 528). The prevalence of penicillin, erythromycin, and cotrimoxazole non-susceptibility was 19% (147/760; 95% CI 17-22%) (3% resistant), 18% (136/760; 95% CI 15-21%) (14% resistant) and 45% (344/760; 95% CI 42-49%) (36% resistant), respectively. The predominant penicillin-non-susceptible serotypes included 15B/15C (n = 20), 19A (n = 13), 15A (n = 10), 19F (n = 8), and 21 (n = 8). Multi-drug resistance (MDR) was observed in 9% (68/760; 95% CI 7-11%) of the isolates. PCV13 serotypes were more likely to be non-susceptible, compared to non-PCV13 serotypes, to penicillin (26% vs. 16%, p = 0.007), erythromycin (23% vs. 15%, p = 0.027) and cotrimoxazole (62% vs. 41%, p < 0.001). Non-susceptibility to penicillin, erythromycin, and cotrimoxazole remained relatively constant through the first year of life (X 2 test for trend: p = 0.184, range 0 – 25%; p = 0.171, range 0 – 27%; and p = 0.572, range 0 – 55%, respectively). Overall, penicillin or erythromycin-non-susceptible pneumococci were carried for a shorter duration than susceptible pneumococci (penicillin [mean days, 18 vs. 21, p = 0.013] and erythromycin [mean days, 18 vs. 21, p = 0.035]). Forty-five percentage (61/137) of infants carried the same serotype which acquired or lost resistance over time, and these changes were predominantly for penicillin (76%, 79/104). Of the 196 NP samples sequenced, 174 had corresponding positive cultures for pneumococci and, of these, 152 were assigned an in-silico serotype. Metagenomic sequencing detected a single pneumococcal serotype in 85% (129/152), and co-colonization in 15% (23/152) of NP samples, respectively. In total, 22 different pneumococcal serotypes were identified, with 15B/15C (n = 49) and 16F (n = 21) being the most common non-PCV13 serotypes, while 23F (n = 9) and 19A (n = 8) were the most common PCV13 serotypes. Twenty-six different sequence types (STs), including 4 novel STs were identified. Mutations in the folA and folP genes, associated with cotrimoxazole resistance, were detected in 89% (87/98) of cotrimoxazole-non-susceptible pneumococci and mutations in the pbp1a and pbp2x genes, known to confer beta-lactam resistance, were identified in penicillin nonsusceptible ST705215B/15C isolates. A total of 329 antimicrobial resistance (AMR) genes were detected in 64% (125/196) of the sequenced samples, including 36 non-redundant genes ranging from 1 to 14 genes per sample. The predominant AMR genes detected were those conferring resistance to beta-lactams (52%, 172/329), macrolide-lincosamide-streptogramin (17%, 56/329), and tetracycline (12%, 38/329). The msrD, ermB, and mefA genes were only detected from pneumococcal reads. The predominant resistance genes detected from nonpneumococcal reads included blaOXA-60, blaOXA-22, and blaBRO-1. Conclusion: NP carriage of antibiotic-non-susceptible pneumococci was relatively constant throughout the first year of life. Despite high vaccine coverage levels, PCV13 serotypes were identified and were more commonly non-susceptible to penicillin, erythromycin, and cotrimoxazole. Overall, penicillin or erythromycin-non-susceptible pneumococci were carried for a shorter duration than susceptible pneumococci, however, non-susceptible PCV13 serotypes were carried for a longer duration than non-susceptible non-PCV13 serotypes. Direct shotgun sequencing from enriched NP samples was shown to be a powerful technique for a detailed description of the pneumococcal component of the NP microbiome and resistome, and its use should be explored similarly for other bacteria in this niche

The clinical spectrum of Staphylococcus Aureus infections in children admitted at Chris Hani Baragwanath Academic Hospital: a retrospective, descriptive study

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfilment of the requirements for the degree of Master of Medicine in the branch of Paediatrics. Johannesburg, March 2018.Introduction: Staphylococcus aureus is a virulent bacterial pathogen which is associated with considerable morbidity and mortality. There are relatively few studies describing invasive S. aureus infections in children, particularly in developing countries. Objectives: To define the spectrum of clinical presentation, risk factors, duration of treatment and outcomes of paediatric S. aureus infections treated at Chris Hani Baragwanath Academic Hospital (CHBAH), South Africa. Methods: A retrospective, descriptive study for the period from January to December 2013 was conducted. Data were sought for all children <14 years of age with S. aureus infection. Results: Four hundred, twenty-two episodes of S. aureus infection were identified. Clinical data were obtained for 286 (68%) cases, on which all further analyses were based. Two-hundred, twenty-six (79%) infections were caused by methicillin-susceptible S. aureus (MSSA), and 60 (21%) were caused by methicillin-resistant S. aureus (MRSA). Clinical presentations for MSSA bacteraemia included skin and soft tissue infection (45%), pneumonia (10%), meningitis (7%), bone/joint infections (5%) and urinary tract infections (4%). Risk factors for MRSA sepsis included burns (OR 38.01; 95%CI 15.33-94.21), prematurity (OR 14.42; 95%CI 5.72-36.34), prolonged hospitalisation (OR 12.26; 95%CI 3.81-40.77), presence of indwelling device (OR 12.08; 95%CI 5.86-24.90) and malnutrition (OR 11.03; 95%CI 3.41-35.74). Five cases of MRSA were attributed to have been community-acquired. Conclusion: Paediatric S. aureus infections are an important cause of morbidity. Most invasive S. aureus infections are caused by methicillin-susceptible strains, although MRSA should be considered particularly in the context of hospitalised patients.LG201

The diagnostic accuracy of the HIV 1/2/subtype O Tri-line HIV rapid test in comparison to ELISA

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfillment of the requirements for the degree of Master of Dentistry. Johannesburg, 2018.Background: Accurate HIV diagnosis is critical and can be life-saving. A Rapid Test (RT) is considered key to HIV prevention and management. Some studies have found RT to be comparable with ELISA whilst others have reported on lower sensitivity. Aim and study design: The aim of this retrospective comparative descriptive study was to evaluate the sensitivity and specificity of the Tri-line HIV rapid test device in comparison to ELISA on patient records from Wits Oral Health Centre (WOHC) between 2014 and 2016 Method: The study population comprised records of patients older than18 months who had Tri-Line HIV RT and blood drawn for ELISA on the same day. Descriptive analysis of the data was carried out. Results: The sensitivity of Tri-line was 80% (CI: 59-93%) and specificity was 100% (CI: 83-100%). The PPV was 100% (CI: 83-100%) and NPV was 80% (CI: 65-90%). ROC area of 0.9 at 95% CI was determined. Conclusion: Due to a low sample size in this study a definitive conclusion could not be drawn. However on the basis of the results obtained, although the tri-line RT showed lower sensitivity it was shown to be a clinically useful test.LG201

Factors affecting sustainability of land reform projects in Ehlanzeni District Mpumalanga Province, South Africa

The study evaluated factors affecting sustainability of land reform projects in Mpumalanga Province in Bushbuckridge Local Municipality (BLM) of Ehlanzeni District. The study was conducted between July and September 2014. A random sampling technique was used in selecting 31 key informants from the projects. Data were collected using face-to-face interviews with key informants that had benefited from the projects using a questionnaire administered as an interview schedule. Data collected were analysed using SPSS. The results shows that both males and females were well represented (50% males) and (50% females), 42% of participants are above 50 years, 83% does not have farming skills, 42% had formal education up to High school level, 75% received agricultural training. Training improved project performance (67%), sustainability (67%), enhanced job creation (58%) and boosted project profitability (92%). 67% received post training support, 92% received training through top down approach. The most factors affecting projects sustainability are lack of government support (75%), failure to receive training on time (75%), and complicated bureaucracy in accessing training (67%).Keywords: Land Reform Projects, Sustainability, Beneficiaries, Agricultural Training, Extension Implications, Ehlanzeni District, South Afric

The politicisation of Funerals in South Africa during the 20th century (1900 – 1994)

The political situation in South Africa since the turn of the 20th century was dominated by two main rivalries: the antagonism between the Afrikaners and the British for the power to rule South Africa, and secondly, the rivalry between the Blacks and the minority White (Afrikaner) Government for the oppressive laws embodied in the policy of apartheid. The situation led to an extent where funerals of both Afrikaners and those of the Blacks were politicised against their respective oppressors. As a concerned citizen and student of History, the researcher set out to critically examine the impact of politicising funerals. The result is this mini-thesis, which is an attempt to understand how politics infiltrated into funerals and how politicising funerals affected political structures as well as close family members. The practice of politicising funerals was noticed in the first quarter of the 20th century amongst funerals of Afrikaner leaders. The anti–British sentiments prevailing at the time were implicitly and explicitly expressed in their funerals. However, as the years progressed, the level of politicising funerals lost spark as they became more religious affairs. While the level of the politicisation of funerals for members of the White community reflects a downward slant, the opposite was the case for the Black community. Politicising funerals in the Black community started on a moderate note and gained momentum and intensity as years progressed. The catalysts to gaining intensity were the 1960 Sharpeville massacres, the 1976 Soweto uprising, the establishment of the UDF in 1983 and the so-called ‘black on black’ violence immediately after the release of Nelson Mandela in 1990. The impact of the Soweto uprising became more conspicuous during Robert Sobukwe’s funeral. Helen Suzman and Benjamin Pogrund, being Whites, were removed from the funeral program while Mangosuthu Buthelezi was chased from the funeral itself. This funeral highlights very well the level of politicisation of funerals during the 1970s. The decade 1980 –1990 witnessed a more aggressive and militant manner of politicising funerals. During that decade, funerals were so popularised that they ‘assumed’ the status of political rallies. The new approach in running funerals was not ended with the release of Mandela in 1990, since there were increasing numbers of funerals of victims of the alleged ‘black on black’ violence. One however welcomes the sombre and respectful manner in which the funerals of Oliver Tambo and Andries Treurnicht were held. The researcher holds the opinion that this should be a trend to follow in future. Politicising funerals dominated the 20th century and in the process affected family members negatively, because they were reduced to passive onlookers.Dissertation (MA (History))--University of Pretoria, 2008.Historical and Heritage Studiesunrestricte

Post settlement challenges for land reform beneficiaries: three case studies from Limpopo Province

Magister Philosophiae (Land and Agrarian Studies) - MPhil(LAS)This thesis presented a study of post-settlement experiences of land reform beneficiaries, with a focus on three case studies from Limpopo Province. Since 1994, the South African government has implemented a land reform programme that aims to redress the injustices in land ownership patterns in the country. This study included a review of international and local literature on land reform with particualr interest in what happens after land transfer and settlement.South Afric

Agrarian change and the fate of farmworkers : trajectories of strategic partnership and farm labour in Levubu Valley, South Africa

Philosophiae Doctor - PhDThis thesis examines the trajectories of agrarian change on community-owned commercial farms in the Levubu Valley in the northern part of Limpopo Province, South Africa. Levubu is a locality where fertile land was developed and made highly productive after state-led dispossession of African communities. White farmers were initially resettled on a state-run irrigation scheme, but later became independent large-scale commercial farmers linked to global agro-food markets. The thesis focusses on four Communal Property Associations (CPAs) that acquired ownership of farms in Levubu. Government’s post-apartheid land restitution programme required the CPAs to enter into ‘strategic partnership’ agreements with agribusiness companies. Resettlement of beneficiaries on these farms was ruled out in an attempt to sustain existing production systems and levels of employment. After these partnerships collapsed, CPAs have attempted to run the farms themselves, through operating companies employing professional farm managers. Using key concepts from agrarian political economy, the thesis seeks to understand the dynamics of production and social reproduction on the farms and the political tensions that have arisen since restitution occurred. It also explores how this form of land restitution has impacted on the livelihoods of farmworkers. The study combines intensive (or qualitative) research methods, involving indepth interviews, focus groups and direct observations, and extensive (or quantitative) approaches, mainly in the form of a farmworker household survey undertaken in two communities. This research design has allowed for ‘retrospective’ analysis of changes over time to be complemented by ‘circumspective’ analysis of the relations and dynamics of property, production and power on community-owned farms in Levubu. The main findings of the study are that neither joint venture companies nor community-owned farming enterprises have been able to distribute dividend payments to claimant community members as yet. Rather, when profits have been realised they have largely been invested back into productive enterprises. Few other benefits have been received either, other than the preferential employment of some claimant farmworkers on the farms, a small number as managers or supervisors. Although additional jobs were created in the initial stages of restitution, these enterprises have struggled to maintain employment levels. Poor management decisions have meant that increased labour costs have not been accompanied by increases in productivity and output. Severe tensions and conflicts have arisen within CPAs, manifested in different forms of identity politics and competing ‘modes of belonging’. Tensions in communityowned large-scale farming enterprises are explained by the contradictory unity of capital and labour within community-owned enterprises, with difficult choices to be made between enhancing social reproduction or ensuring accumulation and profitability. These combine with complex processes of identification in socio-political struggles around access to and control of key resources. These findings suggest that policy makers should re-examine assumptions in relation to community-owned farming enterprises and explore mechanisms through which individual beneficiary households can realise more significant benefits. One policy option might be to seek the complementarity of large-scale commercial farming and smallholder farming systems, both on land restored to CPAs through restitution and in communal areas