Browsing by Author "Van Schalkwyk, Cari"
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- ItemBirth outcomes following antiretroviral exposure during pregnancy : initial results from a pregnancy exposure registry in South Africa(AOSIS, 2019) Mehta, Ushma C.; Van Schalkwyk, Cari; Naidoo, Prineetha; Ramkissoon, Arthi; Mhlongo, Otty; Maharaj, Niren R.; Naidoo, Niree; Fieggen, Karen; Urban, Michael F.; Krog, Shaun; Welte, Alex; Dheda, Mukesh; Pillay, Yogan; Moran, Neil F.Background: In 2013, a pregnancy exposure registry and birth defects surveillance (PER/BDS) system was initiated in eThekwini District, KwaZulu-Natal (KZN), to assess the impact of antiretroviral treatment (ART) on birth outcomes. Objectives: At the end of the first year, we assessed the risk of major congenital malformations (CM) and other adverse birth outcomes (ABOs) detected at birth, in children born to women exposed to ART during pregnancy. Method: Data were collected from women who delivered at Prince Mshiyeni Memorial Hospital, Durban, from 07 October 2013 to 06 October 2014, using medicine exposure histories and birth outcomes from maternal interviews, clinical records and neonatal surface examination. Singleton births exposed to only one ART regimen were included in bivariable analysis for CM risk and multivariate risk analysis for ABO risk. Results: Data were collected from 10 417 women with 10 517 birth outcomes (4013 [38.5%] HIV-infected). Congenital malformations rates in births exposed to Efavirenz during the first trimester (T1) (RR 0.87 [95% CI 0.12–6.4; p = 0.895]) were similar to births not exposed to ART during T1. However, T1 exposure to Nevirapine was associated with the increased risk of CM (RR 9.28 [95% CI 2.3–37.9; p = 0.002]) when compared to the same group. Other ABOs were more frequent in the combination of HIV/ART-exposed births compared to HIV-unexposed births (29.9% vs. 26.0%, adjusted RR 1.23 [1.14–1.31; p < 0.001]). Conclusion: No association between T1 use of EFV-based ART regimens and CM was observed. Associations between T1 NVP-based ART regimen and CM need further investigation. HIV- and ART-exposed infants had more ABOs compared to HIV-unexposed infants.
- ItemHigh human papillomavirus (HPV) prevalence in South African adolescents and young women encourages expanded HPV vaccination campaigns(Public Library of Science, 2018-01-02) Mbulawa, Zizipho Z. A.; Van Schalkwyk, Cari; Hu, Nai-Chung; Meiring, Tracy L.; Barnabas, Shaun; Dabee, Smritee; Jaspan, Heather; Kriek, Jean-Mari; Jaumdally, Shameem Z.; Muller, Etienne; Bekker, Linda-Gail; Lewis, David A.; Dietrich, Janan; Gray, Glenda; Passmore, Jo-Ann S.; Williamson, Anna-LiseThe objectives of the study were to investigate prevalence of cervical human papillomavirus (HPV) genotypes to inform HPV vaccination strategy in South Africa and to study factors associated with HPV prevalence. Sexually active, HIV-negative women, aged 16–22 years recruited from Soweto (n = 143) and Cape Town (n = 148) were tested for cervical HPV and other genital infections. Overall HPV prevalence was 66.7% (194/291) in young women. Cape Town women were more likely to have multiple HPV infections than the Soweto women (48.0%, 71/148 versus 35.0%, 50/143 respectively, p = 0.033) and probable HR-HPV types (34.5%, 51/148 versus 21.7%, 31/143 respectively, p = 0.022). The most frequently detected HPV types were HPV-16 (11.7%), HPV-58 (10.3%), HPV-51 (8.9%), HPV-66 (8.6%), HPV-18 and HPV-81 (7.6% each). HPV types targeted by the bivalent HPV vaccine (HPV-16/18) were detected in 18.6% (54/291) of women, while those in the quadrivalent vaccine (HPV-6/11/16/18) were detected in 24.7% (72/291) of women; and those in the nonavalent vaccine (HPV-6/11/16/18/31/33/45/52/58) were detected in 38.5% (112/291) of women. In a multivariable analysis, bacterial vaginosis remained significantly associated with HPV infection (OR: 4.0, 95% CI: 1.4–12.6). Women were more likely to be HPV positive if they had received treatment for STI during the past 6-months (OR: 3.4, 95% CI: 1.1–12.4) or if they had ever been pregnant (OR: 2.3, 95% CI: 1.1–5.5). Compared to women who reported only one sexual partner, those with increased number of lifetime sex partners were more likely to have HPV (4–10 partners: OR: 2.9, 95% CI: 1.1–8.0). The high prevalence of HPV types targeted by the nonavalent HPV vaccine encourages the introduction of this vaccine and catch-up HPV vaccination campaigns in South Africa. The high burden of BV and concurrent STIs also highlights the need to improve the prevention and appropriate management of sexually-acquired and other genital tract infections in South African youth.
- ItemHigh prevalence of Tuberculosis and insufficient case detection in two communities in the Western Cape, South Africa(PLoS ONE, 2013-04) Claassens, Mareli; Van Schalkwyk, Cari; De Haan, Leonie; Floyd, Sian; Dunbar, Rory; Van Helden, Paul; Godfrey-Faussett, Peter; Ayles, Helen; Borgdorff, Martien; Enarson, Donald; Beyers, NuldaBackground: In South Africa the estimated incidence of all forms of tuberculosis (TB) for 2008 was 960/100000. It was reported that all South Africans lived in districts with Directly Observed Therapy, Short-course. However, the 2011 WHO report indicated South Africa as the only country in the world where the TB incidence is still rising. Aims: To report the results of a TB prevalence survey and to determine the speed of TB case detection in the study communities. Methods: In 2005 a TB prevalence survey was done to inform the sample size calculation for the ZAMSTAR (Zambia South Africa TB and AIDS Reduction) trial. It was a cluster survey with clustering by enumeration area; all households were visited within enumeration areas and informed consent obtained from eligible adults. A questionnaire was completed and a sputum sample collected from each adult. Samples were inoculated on both liquid mycobacterium growth indicator tube (MGIT) and Lo¨ wenstein-Jensen media. A follow-up HIV prevalence survey was done in 2007. Results: In Community A, the adjusted prevalence of culture positive TB was 32/1000 (95%CI 25–41/1000) and of smear positive TB 8/1000 (95%CI 5–13/1000). In Community B, the adjusted prevalence of culture positive TB was 24/1000 (95%CI17–32/1000) and of smear positive TB 9/1000 (95%CI 6–15/1000). In Community A the patient diagnostic rate was 0.38/person-year while in community B it was 0.30/person-year. In both communities the adjusted HIV prevalence was 25% (19–30%). Discussion: In both communities a higher TB prevalence than national estimates and a low patient diagnostic rate was calculated, suggesting that cases are not detected at a sufficient rate to interrupt transmission. These findings may contribute to the rising TB incidence in South Africa. The TB epidemic should therefore be addressed rapidly and effectively, especially in the presence of the concurrently high HIV prevalence.
- ItemIncidence of TB and HIV in prospectively followed household contacts of TB index patients in South Africa(PLoS, 2014-04) Van Schalkwyk, Cari; Variava, Ebrahim; Shapiro, Adrienne E.; Rakgokong, Modiehi; Masonoke, Katlego; Lebina, Limakatso; Welte, Alex; Martinson, NeilObjective: To report the incidence rates of TB and HIV in household contacts of index patients diagnosed with TB. Design: A prospective cohort study in the Matlosana sub-district of North West Province, South Africa. Methods: Contacts of index TB patients received TB and HIV testing after counseling at their first household visit and were then followed up a year later, in 2010. TB or HIV diagnoses that occurred during the period were determined. Results: For 2,377 household contacts, the overall observed TB incidence rate was 1.3 per 100 person years (95% CI 0.9–1.9/100py) and TB incidence for individuals who were HIV-infected and HIV seronegative at baseline was 5.4/100py (95% CI 2.9–9.0/100py) and 0.7/100py (95% CI 0.3–1.4/100py), respectively. The overall HIV incidence rate was 2.2/100py (95% CI 1.3–8.4/100py). Conclusions: In the year following a household case finding visit when household contacts were tested for TB and HIV, the incidence rate of both active TB and HIV infection was found to be extremely high. Clearly, implementing proven strategies to prevent HIV acquisition and preventing TB transmission and progression to disease remains a priority in settings such as South Africa.
- ItemMissed opportunities for retention in pre-ART care in Cape Town, South Africa(Public Library of Science -- PLoS, 2014-05) Du Toit, Elizabeth; Van Schalkwyk, Cari; Dunbar, Rory; Jennings, Karen; Yang, Blia; Coetzee, David; Beyers, Nulda; Fox, MatthewBackground: Few studies have evaluated access to and retention in pre-ART care. Objectives: To evaluate the proportion of People Living With HIV (PLWH) in pre-ART and ART care and factors associated with retention in pre-ART and ART care from a community cohort. Methods: A cross sectional survey was conducted from February – April 2011. Self reported HIV positive, negative or participants of unknown status completed a questionnaire on their HIV testing history, access to pre-ART and retention in pre-ART and ART care. Results: 872 randomly selected adults who reported being HIV positive in the ZAMSTAR 2010 prevalence survey were included and revisited. 579 (66%) reconfirmed their positive status and were included in this analysis. 380 (66%) had initiated ART with 357 of these (94%) retained in ART care. 199 (34%) had never initiated ART of whom 186 (93%) accessed pre-ART care, and 86 (43%) were retained in pre-ART care. In a univariable analysis none of the factors analysed were significantly associated with retention in care in the pre-ART group. Due to the high retention in ART care, factors associated with retention in ART care, were not analysed further. Conclusion: Retention in ART care was high; however it was low in pre-ART care. The opportunity exists, if care is better integrated, to engage with clients in primary health care facilities to bring them back to, and retain them in, pre-ART care.
- ItemModelling of HIV prevention and treatment progress in five South African metropolitan districts(Nature, 2021-03) Van Schalkwyk, Cari; Dorrington, Rob E.; Seatlhodi, Thapelo; Velasquez, Claudia; Feizzadeh, Ali; Johnson, Leigh F.Globally, large proportions of HIV-positive populations live in cities. The Fast-Track cities project aims to advance progress toward elimination of HIV as a public health threat by accelerating the response in cities across the world. This study applies a well-established HIV transmission model to provide key HIV estimates for the five largest metropolitan districts in South Africa (SA): Cape Town, Ekurhuleni, eThekwini, Johannesburg and Tshwane. We calibrate the model to metro-specific data sources and estimate progress toward the 90-90-90 targets set by UNAIDS (90% of people living with HIV (PLHIV) diagnosed, 90% of those diagnosed on antiretroviral therapy (ART) and viral suppression in 90% of those on ART). We use the model to predict progress towards similarly defined 95-95-95 targets in 2030. In SA, 90.5% of PLHIV were diagnosed in 2018, with metro estimates ranging from 86% in Johannesburg to 92% in eThekwini. However, only 68.4% of HIV-diagnosed individuals nationally were on ART in 2018, with the proportion ranging from 56% in Tshwane to 73% in eThekwini. Fractions of ART users who were virally suppressed ranged from 77% in Ekurhuleni to 91% in eThekwini, compared to 86% in the whole country. All five metros are making good progress to reach diagnosis targets and all (with the exception of Ekurhuleni) are expected to reach viral suppression targets in 2020. However, the metros and South Africa face severe challenges in reaching the 90% ART treatment target.
- ItemMortality during tuberculosis treatment in South Africa using an 8-year analysis of the national tuberculosis treatment register(Nature, 2021-08) Osman, Muhammad; Van Schalkwyk, Cari; Naidoo, Pren; Seddon, James A.; Dunbare, Rory; Dlamini, Sicelo S.; Welte, Alex; Hesseling, Anneke C.; Claassens, Mareli M.In 2011, the South African HIV treatment eligibility criteria were expanded to allow all tuberculosis (TB) patients lifelong ART. The impact of this change on TB mortality in South Africa is not known. We evaluated mortality in all adults (≥ 15 years old) treated for drug-susceptible TB in South Africa between 2009 and 2016. Using a Cox regression model, we quantified risk factors for mortality during TB treatment and present standardised mortality ratios (SMR) stratified by year, age, sex, and HIV status. During the study period, 8.6% (219,618/2,551,058) of adults on TB treatment died. Older age, male sex, previous TB treatment and HIV infection (with or without the use of ART) were associated with increased hazard of mortality. There was a 19% reduction in hazard of mortality amongst all TB patients between 2009 and 2016 (adjusted hazard ratio: 0.81 95%CI 0.80–0.83). The highest SMR was in 15–24-year-old women, more than double that of men (42.3 in 2016). Between 2009 and 2016, the SMR for HIV-positive TB patients increased, from 9.0 to 19.6 in women, and 7.0 to 10.6 in men. In South Africa, case fatality during TB treatment is decreasing and further interventions to address specific risk factors for TB mortality are required. Young women (15–24-year-olds) with TB experience a disproportionate burden of mortality and interventions targeting this age-group are needed.
- ItemPatient diagnostic rate as indicator of tuberculosis case detection, South Africa(Centers for Disease Control and Prevention, 2016) Claassens, Mareli; Van Schalkwyk, Cari; Dunbar, Rory; Ayles, Helen; Beyers, NuldaENGLISH SUMMARY : To address the uncertainty of the indirectly measured tuberculosis case detection rate, we used survey data stratified by HIV status to calculate the patient diagnostic rate, a directly measurable indicator, in 8 communities in South Africa. Rates were lower among HIV-negative than HIV-positive persons. Tuberculosis programs should focus on HIV-negative persons.
- ItemPooled PCR testing of dried blood spots for infant HIV diagnosis is cost efficient and accurate(BMC (part of Springer Nature), 2019) Van Schalkwyk, Cari; Maritz, Jean; Van Zyl, Gert U.; Preiser, Wolfgang; Welte, AlexBackground: Access to qualitative HIV PCRs for early infant diagnosis (EID) is restricted in resource-limited settings due to cost. We hypothesised that pooling of dried blood spots (DBS), defined as combining multiple patient samples in a single test with subsequent individual testing of positive pools, would be cost saving while retaining clinical accuracy compared to individual patient testing. Methods: Cost savings: A model was developed to simulate reagent and consumable cost saving of pooled compared to individual sample testing. Daily sample/result data of a public health laboratory in South Africa were used to illustrate outputs from the model. Samples were randomly allocated to pools and the process was repeated 1000 times to measure variation in estimates due to this stochasticity. Clinical accuracy: 1170 patient samples were tested using the Roche CAP/CTM Qual assay in pools of five 50 μl DBS. Negative pools comprised DBS previously tested in single reactions; positive pools included 1 positive sample. Results: Pooling would have saved 64% of laboratory costs in 2015. The model is published as an R-based web tool, into which the user enters sample/positivity estimates and workflow management parameters to obtain cost saving estimates at an optimal pool size. Sensitivity of pooled testing was 98.8% overall; 100% for strongly reactive pools. One pool tested false positive which would not impact clinical specificity as individual patient testing is performed prior to reporting. Conclusions: Pooled PCR testing for EID remains accurate and dramatically reduces costs in settings with moderate to low prevalence rates and sufficient sample numbers.
- ItemProjected early spread of COVID-19 in Africa(2020) Pearson, Carl A. B.; Van Schalkwyk, Cari; Foss, Anna M.; O'Reilly, Kathleen M.; CMMID COVID-19 working group; SACEMA; Pulliam, Juliet R. C.For African countries currently reporting COVID-19 cases, we estimate when they will report more than 1 000 and 10 000 cases. Assuming current trends, more than 80% are likely to exceed 1 000 cases by the end of April 2020, with most exceeding 10 000 a few weeks later.
- ItemTowards eliminating bias in cluster analysis of TB genotyped data(PLOS One, 2012-03) Van Schalkwyk, Cari; Cule, Madeleine; Welte, Alex; Van Helden, Paul; Van Der Spuy, Gian; Uys, PieterThe relative contributions of transmission and reactivation of latent infection to TB cases observed clinically has been reported in many situations, but always with some uncertainty. Genotyped data from TB organisms obtained from patients have been used as the basis for heuristic distinctions between circulating (clustered strains) and reactivated infections (unclustered strains). Naıve methods previously applied to the analysis of such data are known to provide biased estimates of the proportion of unclustered cases. The hypergeometric distribution, which generates probabilities of observing clusters of a given size as realized clusters of all possible sizes, is analyzed in this paper to yield a formal estimator for genotype cluster sizes. Subtle aspects of numerical stability, bias, and variance are explored. This formal estimator is seen to be stable with respect to the epidemiologically interesting properties of the cluster size distribution (the number of clusters and the number of singletons) though it does not yield satisfactory estimates of the number of clusters of larger sizes. The problem that even complete coverage of genotyping, in a practical sampling frame, will only provide a partial view of the actual transmission network remains to be explored.
- ItemTuberculosis in healthcare workers and infections control measures at primary healthcare facilities in South Africa(Public Library of Science, 2013-10-02) Claassens, Mareli; Van Schalkwyk, Cari; Du Toit, Elizabeth; Roest, Eline; Lombard, Carl J.; Enarson, Donald A.; Beyers, Nulda; Borgdorff, Martien W.Background Challenges exist regarding TB infection control and TB in hospital-based healthcare workers in South Africa. However, few studies report on TB in non-hospital based healthcare workers such as primary or community healthcare workers. Our objectives were to investigate the implementation of TB infection control measures at primary healthcare facilities, the smear positive TB incidence rate amongst primary healthcare workers and the association between TB infection control measures and all types of TB in healthcare workers. Methods One hundred and thirty three primary healthcare facilities were visited in five provinces of South Africa in 2009. At each facility, a TB infection control audit and facility questionnaire were completed. The number of healthcare workers who had had TB during the past three years was obtained. Results The standardised incidence ratio of smear positive TB in primary healthcare workers indicated an incidence rate of more than double that of the general population. In a univariable logistic regression, the infection control audit score was significantly associated with reported cases of TB in healthcare workers (OR=1.04, 95%CI 1.01-1.08, p=0.02) as was the number of staff (OR=3.78, 95%CI 1.77-8.08). In the multivariable analysis, the number of staff remained significantly associated with TB in healthcare workers (OR=3.33, 95%CI 1.37-8.08). Conclusion The high rate of TB in healthcare workers suggests a substantial nosocomial transmission risk, but the infection control audit tool which was used did not perform adequately as a measure of this risk. Infection control measures should be monitored by validated tools developed and tested locally. Different strategies, such as routine surveillance systems, could be used to evaluate the burden of TB in healthcare workers in order to calculate TB incidence, monitor trends and implement interventions to decrease occupational TB.
- ItemUnderstanding and acting on the developmental origins of health and disease in Africa would improve health across generations(Taylor & Francis Open, 2017) Norris, Shane A.; Daar, Abdallah; Balasubramanian, Dorairajan; Byass, Peter; Kimani-Murage, Elizabeth; Macnab, Andrew; Pauw, Christoff; Singhal, Atul; Yajnik, Chittaranjan; Akazili, James; Levitt, Naomi; Maatoug, Jihene; Mkhwanazi, Nolwazi; Moore, Sophie E.; Nyirenda, Moffat; Pulliam, Juliet R. C.; Rochat, Tamsen; Said-Mohamed, Rihlat; Seedat, Soraya; Sobngwi, Eugene; Tomlinson, Mark; Toska, Elona; Van Schalkwyk, CariData from many high- and low- or middle-income countries have linked exposures during key developmental periods (in particular pregnancy and infancy) to later health and disease. Africa faces substantial challenges with persisting infectious disease and now burgeoning non-communicable disease.This paper opens the debate to the value of strengthening the developmental origins of health and disease (DOHaD) research focus in Africa to tackle critical public health challenges across the life-course. We argue that the application of DOHaD science in Africa to advance life-course prevention programmes can aid the achievement of the Sustainable Development Goals, and assist in improving health across generations. To increase DOHaD research and its application in Africa, we need to mobilise multisectoral partners, utilise existing data and expertise on the continent, and foster a new generation of young African scientists engrossed in DOHaD.
- ItemWing length and host location in tsetse (Glossina spp.) : implications for control using stationary baits(BMC (part of Springer Nature), 2019-01-11) Hargrove, John W.; English, Sinead; Torr, Stephen J.; Lord, Jennifer; Haines, Lee Rafuse; Van Schalkwyk, Cari; Patterson, James; Vale, GlynBackground: It has been suggested that attempts to eradicate populations of tsetse (Glossina spp.) using stationary targets might fail because smaller, less mobile individuals are unlikely to be killed by the targets. If true, tsetse caught in stationary traps should be larger than those from mobile baits, which require less mobility on the part of the flies. Results: Sampling tsetse in the Zambezi Valley of Zimbabwe, we found that the number of tsetse caught from stationary traps, as a percent of total numbers from traps plus a mobile vehicle, was ~5% for male G. morsitans morsitans (mean wing length 5.830 mm; 95% CI: 5.800–5.859 mm) and ~10% for females (6.334 mm; 95% CI: 6.329– 6.338 mm); for G. pallidipes the figures were ~50% for males (6.830 mm; 95% CI: 6.821–6.838 mm) and ~75% for females (7.303 mm, 95% CI: 7.302–7.305 mm). As expected, flies of the smaller species (and the smaller sex) were less likely to be captured using stationary, rather than mobile sampling devices. For flies of a given sex and species the situation was more complex. Multivariable analysis showed that, for females of both species, wing lengths changed with ovarian age and the month, year and method of capture. For G. pallidipes, there were statistically significant interactions between ovarian age and capture month, year and method. For G. m. morsitans, there was only a significant interaction between ovarian age and capture month. The effect of capture method was, however, small in absolute terms: for G. pallidipes and G. m. morsitans flies caught on the mobile vehicle had wings only 0.24 and 0.48% shorter, respectively, than flies caught in stationary traps. In summary, wing length in field samples of tsetse varies with ovarian age, capture month and year and, weakly, with capture method. Suggestions that a target-based operation against G. f. fuscipes in Kenya caused a shift towards a smaller, less mobile population of tsetse, unavailable to the targets, failed to account for factors other than capture method. Conclusions: The results are consistent with the successful use of targets to eradicate populations of tsetse in Zimbabwe. Until further, more nuanced, studies are conducted, it is premature to conclude that targets alone could not, similarly, be used to eradicate G. f. fuscipes populations in Kenya.