Patterns of oxygen saturation in prolonged recovery from COVID-19 pneumonia.

During the second wave of the COVID-19 pandemic in South Africa, a recurrent pattern of prolonged recovery after acute COVID-19 pneumonia, characterised by low oxygen saturation levels for >2 weeks, was observed in an intermediate-care facility in Cape Town. A case study together with a series of 12 patients is presented to illustrate this phenomenon, and two types of 'sats gap' are described, which were used by physiotherapists and doctors to monitor daily progress. We attempt to explain this prolonged recovery in terms of the possible pathophysiology, and suggest a number of learning points to guide further research.

Do electronic patient information systems improve efficiency and quality of care? An evaluation of utilisation of the Discovery HealthID application.

BACKGROUND: Electronic health records (EHRs) appear to offer a number of potential benefits, but practitioners are often hesitant to make the transition to using them. OBJECTIVES: To determine whether the use of one such system, designed and offered by a health insurer (HealthID; Discovery Health), makes a difference to the efficiency and quality of doctor-patient consultations. METHODS: A descriptive study using mixed methods was designed. A qualitative phase of individual interviews of purposefully sampled respondents was followed by a quantitative survey of a random sample of general practitioners and specialists who were registered users of the system. RESULTS: In the qualitative findings, 18 respondents reported their perceptions of the ease of use of the application, their motivation for using it, its functions and benefits, the impact on efficiency and quality of care, and the challenges they experienced. In addition, they reported on the details of the challenges of using the system, and made suggestions for improvements, particularly with regard to the need for training and IT support. The quantitative results from the majority of 93 respondents confirmed that while the use of the app improved patient care through positive effects on specific functions such as access to accurate patient records and easier Chronic Illness Benefit applications, they felt that it had an equivocal impact in other areas, such as maintaining patient confidentiality and enhancing teamwork and efficiency. The financial incentives offered by Discovery Health, as well as possibly the training and support provided, appear to be more influential for high-frequency than for low-frequency users. The majority said that it did not help with referrals or script writing, or with access to International Statistical Classification of Diseases and Related Health Problems, 10th revision (ICD-10) codes. CONCLUSIONS: EHR systems like Discovery Health's HealthID could improve the efficiency of medical consultations by increasing access to stored health information without requiring data entry by clinicians, and thereby have the potential to indirectly improve the quality of care, provided that certain conditions are met.

Compulsory community service for doctors in South Africa: A 15-year review.

BACKGROUND: Compulsory community service (CS) for health professionals for 12 months was introduced in South Africa (SA) in 1998, starting with medical practitioners. Up to 2014, a total of 17 413 newly qualified doctors and ~44 000 health professionals had completed their year of service in public health facilities around the country. While a number of studies have described the experience and effects of CS qualitatively, none has looked at the programme longitudinally. OBJECTIVES: To describe the findings and analyse trends from surveys of CS doctors between 2000 and 2014, specifically with regard to their distribution, support, feedback and career plans. METHODS: A consecutive cross-sectional descriptive study design was used based on annual national surveys of CS doctors. The study population of between 1 000 and 1 300 each year was surveyed with regard to their origins, allocations, experiences of the year and future career plans. RESULTS: The total study population varied between 1 057 and 1 308 each year, with response rates of 20 - 77%. The average turn-up rate of 89% showed a decreasing tendency, while 77% of respondents were satisfied with the allocation process. Over the 15-year period, the proportion of CS doctors who were black and received a study bursary, and who were allocated to rural areas and district hospitals, increased. The great majority believed that they had made a difference (91%) and developed professionally (81%) over the course of the year, but only about half felt adequately supported clinically and administratively. The attitude towards CS of the majority of respondents shifted significantly from neutral to positive over the course of the 15 years. In terms of future career plans, 50% hoped to specialise, a decreasing minority to go overseas or into private practice, and a constant 15% to work in rural or underserved areas. CONCLUSIONS: This study is the first to track the experience of compulsory CS over time in any country in order to describe the trends once it had become institutionalised. The SA experience of CS for doctors over the first 15 years appears to have been a successively positive one, and it has largely met its original objectives of redistribution of health professionals and professional development. Greater attention needs to be given to orientation, management support and clinical supervision, and focusing professional development opportunities on the important minority who are prepared to stay on longer than their obligatory year. CS still needs to be complemented by other interventions to capitalise on its potential.

Toxin A-negative toxin B-positive ribotype 017 Clostridium difficile is the dominant strain type in patients with diarrhoea attending tuberculosis hospitals in Cape Town, South Africa.

The molecular epidemiology of C. difficile strains causing disease in South Africa is currently unknown. Previously, multidrug resistant ribotype (RT)017 strains were those most commonly isolated from patients with diarrhoea attending Groote Schuur Hospital in Cape Town, South Africa. This larger study aimed to investigate the molecular epidemiology and antibiotic susceptibility profiles of C. difficile strains in the greater Cape Town and regional areas. C. difficile strains were isolated from patients with diarrhoea attending hospitals in the Western Cape region of South Africa that tested positive using the GeneXpert CDiff diagnostic test. Ribotyping and multilocus variable-number tandem-repeat analysis (MLVA) were used to type isolates, and their susceptibilities to several antibiotics were determined by gradient diffusion test strips. A total of 269 non-repeat C. difficile isolates were obtained. A large proportion of isolates (64.3 %) belonged to the RT017 group, many of which were clonally related when investigated by MLVA. RT017 strains were particularly prevalent in patients attending specialist tuberculosis (TB) hospitals. The majority of RT017 isolates were co-resistant to moxifloxacin and rifampicin, two antibiotics which are used intensively during anti-TB therapy. Non-RT017 strains were generally susceptible to both antibiotics. Resistance to erythromycin was observed for both groups of strains. RT017 C. difficile strains are the most commonly isolated strains from patients attending healthcare facilities in the greater Cape Town and regional areas. The presence of multidrug resistant RT017 strains in patients with diarrhoea attending local TB hospitals reflects a potential reservoir for future infections.

Glutamate and histidine improve both solvent yields and the acid tolerance response of Clostridium beijerinckii NCP 260.

AIMS: This study aims to examine the effect of amino acid supplementation on solvent production by Clostridium beijerinckii during the acetone-butanol fermentation and to determine whether amino acids are involved in the acid tolerance response (ATR), which results in increased solvents. METHODS AND RESULTS: Fermentation studies with Cl. beijerinckii NCP 260 in limited-nitrogen media supplemented with glutamate, glutamine, lysine, proline, histidine or asparagine revealed that only glutamate, glutamine or histidine increased butanol titres comparable to control media. Acid survival tests at pH 5 showed that glutamate and histidine were effective in protecting Cl. beijerinckii cells against acid shock, and may be involved in the ATR. Using quantitative PCR, the transcription of the glutamine synthetase, nitrogen regulator and glutamate synthase operon (glnA-nitR-gltAB) was monitored during acid shock conditions, and expression of both the nitR and gltA genes was shown to be increased twofold. CONCLUSIONS: Glutamate and histidine specifically enhance the ATR in Cl. beijerinckii NCP 260, and the genes encoding glutamate synthase and the NitR regulator are both upregulated, predicted to lead to increased endogenous glutamate pools during acidogenesis. This may enhance the ATR and allow more viable cells to enter solventogenesis, thereby increasing butanol titres. Glutamine, glutamate and histidine may also afford protection from butanol stress directly. SIGNIFICANCE AND IMPACT OF THE STUDY: Using substrates naturally rich in glutamine, glutamate and histidine in industrial fermentations is a promising means to increase acid survival and solvent yields in solventogenic Clostridium.

A functional analysis of the formyl-coenzyme A (frc) gene from Lactobacillus reuteri 100-23C.

AIM: To examine the role of the Lactobacillus reuteri 100-23C frc gene product in oxalate metabolism, host colonization and the acid stress response. METHODS AND RESULTS: Genes encoding putative formyl-CoA transferase (frc) and oxalyl-CoA decarboxylase (oxc) enzymes are present in the genome sequences of Lact. reuteri strains. Two strains isolated from humans harboured an IS200 insertion sequence in the frc ORF and a group 2 intron-associated transposase downstream of the frc gene, both of which were lacking in two strains of animal origin, which contained intact frc and oxc genes. An frc(-) insertional mutant of Lact. reuteri 100-23C was compared with the parent strain with respect to oxalate degradation, colonization of an RLF-mouse host model and growth in the presence of acids. Neither parent nor mutant degraded oxalate in vitro or in vivo. However, the parent outcompeted the frc(-) mutant in the mouse intestine during co-colonization and the frc(-) mutant showed a reduced growth rate in the presence of hydrochloric acid. CONCLUSIONS: Intact oxc and frc genes do not ensure oxalate degradation under the conditions tested. The frc gene product is important during host colonization and survival of acid stress by Lact. reuteri 100-23C. SIGNIFICANCE AND IMPACT OF THE STUDY: Oxalate metabolism by oxalate-degrading intestinal bacterial strains may be important in preventing urolithiasis and might lead to the derivation of probiotic products. To produce safe and efficacious probiotics, however, an understanding of the genetic characteristics of potential oxalate degraders must be obtained, together with knowledge of their functional ramifications.

Diversity of faecal oxalate-degrading bacteria in black and white South African study groups: insights into understanding the rarity of urolithiasis in the black group.

AIM: To examine whether enhanced diversity or numbers of oxalate-degrading bacteria in the gastrointestinal tracts of black South Africans play a role in determining the rarity of urolithiasis in this group. METHODS AND RESULTS: Fresh faecal samples collected from healthy black and white South African male volunteers were analysed in terms of bacterial oxalate-degrading activity, bacterial diversity and relative species abundance. Varied bacterial populations prepared from samples from the low-risk black group showed a significantly higher level of oxalate degradation. Denaturing gradient gel electrophoresis analyses of Lactobacillus and related spp. and Bifidobacterium spp. 16S rRNA PCR products revealed a significantly higher faecal Lactobacillus diversity for the low-risk black group relative to the higher-risk white group. Quantitative real-time PCR experiments did not show any significant differences between the study groups for Lactobacillus and related spp.. However, Bifidobacterium spp. were present at a significantly higher relative abundance in the black group. Oxalobacter formigenes was present only at very low levels in either group. CONCLUSIONS: The low abundance of O. formigenes and increased diversity and abundance of oxalate-degrading Lactobacillus and Bifidobacterium spp. in the black South African population suggest that these strains rather than O. formigenes may protect this group against calcium oxalate kidney stone disease. SIGNIFICANCE AND IMPACT OF THE STUDY: The South African black population harbours a pool of potential oxalate-degrading lactic acid bacteria, which is more abundant and diverse than that of white South Africans. This may be useful in developing probiotics for calcium oxalate kidney stone prophylaxis.

Educational factors that influence the urban-rural distribution of health professionals in South Africa: a case-control study.

SETTING: The influence of undergraduate and postgraduate training on health professionals' career choices in favour of rural and underserved communities has not been clearly demonstrated in resource-constrained settings. OBJECTIVES: This study aimed to evaluate the influence of educational factors on the choice of rural or urban sites of practice of health professionals in South Africa. METHODS: Responses to a questionnaire on undergraduate and postgraduate educational experiences by 174 medical practitioners in rural public practice were compared with those from 142 urban public hospital doctors. Outcomes measured included specific undergraduate and postgraduate educational experiences, and non-educational factors such as family and community influences that were likely to affect the choice of the site of practice. RESULTS: Compared with urban doctors, rural respondents were significantly less experienced, more likely to be black, and felt significantly more accountable to the community that they served. They were more than twice as likely as the urban group to have been exposed to rural situations during their undergraduate training, and were also five times more likely than urban respondents to state that exposure to rural practice as an undergraduate had influenced their choice of where they practise. Urban respondents were significantly more attracted to working where they do by professional development and postgraduate education opportunities and family factors than the rural group. CONCLUSIONS: Evidence is provided that rural exposure influences the choice of practice site by health professionals in a developing country context, but the precise curricular elements that have the most effect deserve further research.

The contribution of South African curricula to prepare health professionals for working in rural or under-served areas in South Africa: a peer review evaluation.

SETTING: The Collaboration for Health Equity through Education and Research (CHEER) was formed in 2003 to examine strategies that would increase the production of health professionals who choose to practise in rural and under-served areas in South Africa. OBJECTIVES: We aimed to identify how each faculty is preparing its students for service in rural or under-served areas. METHODS: Peer reviews were conducted at all nine participating universities. A case study approach was used, with each peer review constituting its own study but following a common protocol and tools. Each research team comprised at least three reviewers from different universities, and each review was conducted over at least 3 days on site. The participating faculties were assessed on 11 themes, including faculty mission statements, resource allocation, student selection, first exposure of students to rural and under-served areas, length of exposure, practical experience, theoretical input, involvement with the community, relationship with the health service, assessment of students and research and programme evaluation. RESULTS: With a few exceptions, most themes were assessed as inadequate or adequate with respect to the preparation of students for practice in rural or under-served areas after qualification, despite implicit intentions to the contrary at certain faculties. CONCLUSIONS: Common challenges, best practices and potential solutions have been identified through this project. Greater priority must be given to supporting rural teaching sites in terms of resources and teaching capacity, in partnership with government agencies.

Equine parascarosis under the tropical weather conditions of Ethiopia: a coprological and postmortem study.

A cross-sectional coprological survey in the regions of Ada, Akaki, Bereh and Boset, and a retrospective postmortem investigation were conducted to study the epidemiology of Parascaris equorum in donkeys and horses in Ethiopia. Faecal samples from 803 working donkeys and 402 horses were collected, and the numbers of worms recovered from 112 donkeys examined postmortem between 1995 and 2004 were analysed. There was a high prevalence of infection and faecal egg output of P equorum in both donkeys and horses, and the severity of the infection in donkeys was increased irrespective of their age. The prevalence of the infection in the donkeys was 51.1 per cent and in the horses 16.2 per cent, and the prevalence in the donkeys examined postmortem was 55 per cent. There was no significant difference between different age groups of donkeys in either the prevalence or the intensity of the infection. The prevalence of the infection was significantly higher in the Ada and Akaki regions than in the Bereh and Boset regions.

A functional analysis of the Bifidobacterium longum cscA and scrP genes in sucrose utilization.

The role of genes involved in sucrose catabolism was investigated with a view to designing effective prebiotic substrates to encourage the growth of Bifidobacterium in the gut. Two gene clusters coding for sucrose utilisation in Bifidobacterium longum NCC2705 were identified in the published genome. The genes encoding putative sucrose degrading enzymes, namely, the scrP (sucrose phosphorylase) and the cscA (beta-fructofuranosidase), were cloned from B. longum NCIMB 702259(T) and expressed in Escherichia coli DH5alpha. Both complemented the sucrase negative phenotype of untransformed cells and showed specific sucrase activity. Transcriptional analysis of the expression of the genes in B. longum grown in the presence of various carbohydrate substrates showed induction of scrP gene expression in the presence of sucrose and raffinose, but not in the presence of glucose. The cscA gene showed no increased transcription in B. longum grown in the presence of any of the carbohydrates tested. Phylogenetic analysis indicates that the B. longum CscA protein belongs to a distinct phylogenetic cluster of intracellular fructosidases, which specifically cleave the shorter fructose oligosaccharides.

The community involvement of nursing and medical practitioners in KwaZulu-Natal

Background: The basis of the health system in South Africa is purported to be primary health care (PHC); as defined by the Alma Ata Declaration of 1978. This approach emphasises community involvement in all health-related activities; but it would appear that a very limited or selective PHC approach is actually being pursued in South Africa; without meaningful community participation or ownership. This study explores the involvement of exemplary medical and nursing clinical practitioners in non-clinical community-wide activities in terms of the primary health care approach; which demands a broader scope of practice than primary medical care. Methods: The objectives of the study were to identify exemplary medical and nurse practitioners in primary health care; to document their practices and perceptions with regard to their community involvement; to analyse the common themes arising from the findings; and to present recommendations based on the findings. Seventeen primary care clinicians in KwaZulu-Natal; half of whom were professional nurses and the rest medical practitioners; were purposively selected through their district managers. A team of four medical students was trained to collect the data and interviewed the subjects in their places of work using open-ended questions. The interviews were recorded; translated where necessary; and transcribed. Content analysis was carried out as a team; with the identification of major and minor themes.Results: The findings of this study were consistent with studies from other countries; with some interesting differences. The major themes that emerged from the data included the wide range of activities that subjects were involved in; the importance of relationships; the context of poverty; the frustrations of this kind of work; and the respondents' motivations. These are illustrated by numerous verbatim quotes from the respondents. Minor themes were the roles that the respondents play in the community; the difficulty of obtaining funding; and experiences in starting up. Significantly; the fact that the role of clinicians in the community emerged as only a minor theme rather than a major theme in this study indicates the absence of expectation and policy in this area of practice in South Africa. In the light of the supposed centrality of the primary healthcare approach in the national health system; this is a serious gap.Conclusion: The lack of a clearly defined role in the community outside of the clinical role that deals with the individual patient who presents for care is discussed in relation to the policy of the primary health care approach. The concept of community-oriented primary care provides a framework for a more systematic approach to community engagement; and this study serves as a basis for further research into the subject

Use of traditional African fermented beverages as delivery vehicles for Bifidobacterium lactis DSM 10140.

A microencapsulation delivery system for Bifidobacterium lactis, a possible probiotic suited for use by the rural population of South Africa, was evaluated using two existing traditional fermented foods, amasi and mahewu. Gellan/xanthan microcapsules containing viable B. lactis, were tested under simulated physiological conditions, and added to pasteurized beverages. The capsules protected the organism under simulated low pH conditions associated with the stomach and from the biocidal activity of pancreatic and bile acids. For mahewu, microencapsulation of B. lactis with storage aerobically at 4 degrees C and 22 degrees C enhanced survival over a 21-day period as compared to free cells. In amasi, differences in viability between immobilized and free cells were less noticeable. An analytically trained taste panel was unable to detect a significant difference in texture in any of the samples fortified with microcapsules. Although flavour differences were noted for mahewu containing either free or immobilized cells, after 14 days refrigerated storage, these were not disliked. No significant flavour difference was noted between amasi containing immobilized cells and untreated controls over the period tested.

TATA-binding protein in neurodegenerative disease.

TATA binding protein (TBP) is a general transcription factor that plays an important role in initiation of transcription. In recent years evidence has emerged implicating TPB in the molecular mechanism of a number of neurodegenerative diseases. Wild type TBP in humans contains a long polyglutamine stretch ranging in size from 29 to 42. It has been found associated with aggregated proteins in several of the polyglutamine disorders. Expansion in the CAA/CAG composite repeat beyond 42 has been shown to cause a cerebellar ataxia, SCA17. The involvement of such an important housekeeping protein in the disease mechanism suggests a major impact on the functioning of cells. The question remains, does TBP contribute to these diseases through a loss of normal function, likely to be catastrophic to a cell, or the gain of an aberrant function? This review deals with the function of TBP in transcription and cell function. The distribution of the polyglutamine coding allele lengths in TBP of the normal population and in SCA17 is reviewed and an outline is given on the reported cases of SCA17. The role of TBP in other polyglutamine disorders will be addressed as well as its possible role in other neurodegenerative diseases.

Nitrogen and carbon regulation of glutamine synthetase and glutamate synthase in Corynebacterium glutamicum ATCC 13032.

The effect of nitrogen and carbon status on the regulation of glutamine synthetase (GS) and glutamate synthase (GOGAT) were investigated in Corynebacterium glutamicum 13032. Under carbon-sufficient, nitrogen-limiting conditions, GS and GOGAT activities were five- and seven-fold higher, respectively, and transcription of the corresponding genes (glnA and gltBD) was similarly induced. GS activity was also induced in complete medium with added glucose, while GOGAT activity was unaffected. Under carbon-limiting, nitrogen-limiting conditions, the level of GS induction was reduced approximately three-fold, whereas GOGAT activity did not respond. Disruption of the hkm gene, encoding a putative histidine kinase upstream of gltBD, reduced the levels of GOGAT activity two-fold under both nitrogen-rich and nitrogen-limiting conditions. Promoter studies using a hkm-chloramphenicol acetylase fusion plasmid revealed that transcription of hkm is moderately induced (ca. 1.5-fold) by nitrogen starvation, indicating that the Hkm protein may play a role in signal transduction of the nutritional status of the growth medium.

Invasive pneumococcal disease in the Northern Territory of Australia, 1994-1998.

OBJECTIVE: To examine the epidemiology of invasive pneumococcal disease (IPD) in the Northern Territory of Australia as a basis for optimising vaccination and healthcare provision. DESIGN: Prospective laboratory surveillance, with information collected from hospital and clinic records. SETTING: Northern Territory (NT) and rural communities in north-west South Australia served by an NT hospital, 1994-1998 (NT population is 27% Indigenous). MAIN OUTCOME MEASURES: IPD incidence and mortality, risk factors, clinical presentation and disease-causing serotypes in Indigenous and non-Indigenous people. RESULTS: 425 cases of IPD were detected, with 77% in Indigenous people. IPD incidence was highest in Indigenous children aged < 2 years (1534 per 100,000 in central Australia), but about 100 per 100,000 in non-Indigenous children < 2 years and all Indigenous age groups aged > or = 15 years. Mean ages of those with disease were 39 years in Indigenous people and 48 years in non-Indigenous people (P = 0.006) and, of those who died, 41 and 53 years, respectively (P = 0.04). IPD risk factors were present in 72% of Indigenous and 55% of non-Indigenous patients aged > or = 2 years. Serotype results for 363 isolates showed that the 23-valent vaccine covered 68% and 85% of isolates from Indigenous and non-Indigenous people aged > or = 2 years, respectively, while the proposed seven-, nine- and 11-valent conjugate vaccines covered 58%, 66% and 67% of isolates, respectively, from Indigenous children aged < 2 years and 72% each of those from non-Indigenous children. Case-fatality rates were 10% in both Indigenous and non-Indigenous people. CONCLUSION: These data support the recent change in NT vaccination policy which extended funding for the 23-valent vaccine to all Indigenous people aged > or = 15 years and all Indigenous children in central Australia aged 2-5 years. The high rates of IPD in both Indigenous and non-Indigenous children mandate action to make conjugate vaccine available as soon as possible.

Construction of a reporter gene vector for Clostridium beijerinckii using a Clostridium endoglucanase gene.

A beta-1,4-endoglucanase gene (eglA) cloned from C. acetobutylicum P262 was selected for use in the development of a reporter system for C. beijerinckii NCIMB 8052. The reporter plasmid, pER1, was constructed by ligating the promoterless eglA gene into the B subtilis/Clostridium shuttle vector, pFNK1, which can replicate and is stably maintained in C. beijerinckii. The expression of the endoglucanase enzyme from its own promoter was not significantly induced in cells grown in glucose, sucrose or galactose, while growth of cells in cellobiose or fructose resulted in lower levels of activity. The enzyme was efficiently secreted into the culture medium and did not remain associated with the cell in any way. A transcriptional fusion between the glutamine synthetase (glnA) promoter region and the promoterless eglA gene resulted in high levels of endoglucanase expression, which reflected an 11-fold increase in expression levels over the eglA promoter.