A New Tetrahymena (Ciliophora,Oligohymenophorea) from Groundwater of Cape Town,South Africa

The identification of species within the genus Tetrahymena is known to be difficult due to their essentially identical morphology, the occurrence of cryptic and sibling species and the phenotypic plasticity associated with the polymorphic life cycle of some species. We have combined morphology and molecular biology to describe Tetrahymena aquasubterranea n. sp. from groundwater of Cape Town, Republic of South Africa. The phylogenetic analysis compares the cox1 gene sequence of T. aquasubterranea with the cox1 gene sequences of other Tetrahymena species and uses the interior‐branch test to improve the resolution of the evolutionary relationships. This showed a considerable genetic divergence of T. aquasubterranea to its next relative, T. farlyi, of 9.2% (the average cox1 divergence among bona fide species of Tetrahymena is ~ 10%). Moreover, the analysis also suggested a sister relationship between T. aquasubterranea and a big clade comprising T. farleyi, T. tropicalis, T. furgasoni and T. mobilis. The morphological data available for these species show that they share with T. aquasubterranea a pyriformis‐like life style and at least two of them, T. farleyi and T. mobilis, a similar type II silverline pattern consisting of primary and secondary meridians. Tetrahymena aquasubterranea exhibits a biphasic life cycle with trophonts and theronts, is amicronucleate, and feeds on bacteria.     

Missed Opportunities for Retention in Pre-ART Care in Cape Town,South Africa

Background

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.     

Linkage to HIV care and antiretroviral therapy in Cape Town, South Africa

Background

Antiretroviral therapy (ART) has been scaled-up rapidly in Africa. Programme reports typically focus on loss to follow-up and mortality among patients receiving ART. However, little is known about linkage and retention in care of individuals prior to starting ART.

Methodology

Data on adult residents from a periurban community in Cape Town were collected at a primary care clinic and hospital. HIV testing registers, CD4 count results provided by the National Health Laboratory System and ART registers were linked. A random sample (n = 885) was drawn from adults testing HIV positive through antenatal care, sexual transmitted disease and voluntary testing and counseling services between January 2004 and March 2009. All adults (n = 103) testing HIV positive through TB services during the same time period were also included in the study. Linkage to HIV care was defined as attending for a CD4 count measurement within 6 months of HIV diagnosis. Linkage to ART care was defined as initiating ART within 6 months of HIV diagnosis in individuals with a CD4 count ≤200 cells/µl taken within 6 months of HIV diagnosis.

Findings

Only 62.6% of individuals attended for a CD4 count measurement within 6 months of testing HIV positive. Individuals testing through sexually transmitted infection services had the best (84.1%) and individuals testing on their own initiative (53.5%) the worst linkage to HIV care. One third of individuals with timely CD4 counts were eligible for ART and 66.7% of those were successfully linked to ART care. Linkage to ART care was highest among antenatal care clients. Among individuals not yet eligible for ART only 46.3% had a repeat CD4 count. Linkage to HIV care improved in patients tested in more recent calendar period.

Conclusion

Linkage to HIV and ART care was low in this poor peri-urban community despite free services available within close proximity. More efforts are needed to link VCT scale-up to subsequent care.     

Two remarkable new species of Penicillata (Diplopoda, Polyxenida) from Table Mountain National Park (Cape Town, South Africa)

Two new species of the families Polyxenidae and Synxenidae, are described from Table Mountain National Park, South Africa. Propolyxenus squamatussp. n. (Polyxenidae) has tergites I-X mostly covered by scale-shaped trichomes directed caudally, a character previously known only in Synxenidae. The structure of scale-shaped dorsal trichomes is different to that of the scales in Phryssonotus and Condexenus species. Phryssonotus brevicapensissp. n. (Synxenidae) is the only known species of the genus Phryssonotus having 11 tergites, (including collum and telson) and 15 pairs of legs, as in Condexenus biramipalpus Nguyen Duy-Jacquemin, 2006. These two species therefore appear to occupy an intermediate position between Phryssonotus (12 tergites) and Polyxenoidea (maximum of 11 tergites).     

Prevalence, causes and socio-economic determinants of vision loss in Cape Town, South Africa

Purpose

To estimate the prevalence and causes of blindness and visual impairment in Cape Town, South Africa and to explore socio-economic and demographic predictors of vision loss in this setting.

Methods

A cross sectional population-based survey was conducted in Cape Town. Eighty-two clusters were selected using probability proportionate to size sampling. Within each cluster 35 or 40 people aged 50 years and above were selected using compact segment sampling. Visual acuity of participants was assessed and eyes with a visual acuity less than 6/18 were examined by an ophthalmologist to determine the cause of vision loss. Demographic data (age, gender and education) were collected and a socio-economic status (SES) index was created using principal components analysis.

Results

Out of 3100 eligible people, 2750 (89%) were examined. The sample prevalence of bilateral blindness (presenting visual acuity <3/60) was 1.4% (95% CI 0.9–1.8). Posterior segment diseases accounted for 65% of blindness and cataract was responsible for 27%. The prevalence of vision loss was highest among people over 80 years (odds ratio (OR) 6.9 95% CI 4.6–10.6), those in the poorest SES group (OR 3.9 95% CI 2.2–6.7) and people with no formal education (OR 5.4 95% CI 1.7–16.6). Cataract surgical coverage was 68% in the poorest SES tertile (68%) compared to 93% in the medium and 100% in the highest tertile.

Conclusions

The prevalence of blindness among people ≥50 years in Cape Town was lower than expected and the contribution of posterior segment diseases higher than previously reported in South Africa and Sub Saharan Africa. There were clear socio-economic disparities in prevalence of vision loss and cataract surgical coverage in this setting which need to be addressed in blindness prevention programs.     

Macroinvertebrate communities associated with duckweed (Lemnaceae) in two Eastern Cape rivers,South Africa

The functional feeding groups and diversity of macroinvertebrate communities associated with duckweed mats in the New Years River (two sites) and Bloukrans River (two sites), Eastern Cape province, South Africa, were assessed. Duckweed (Lemnaceae) is a ubiquitous family of floating macrophytes. A total of 41 macroinvertebrate families were collected monthly over a six-month period from February to July 2014. Duckweed biomass in both rivers was highly variable both temporally and spatially. The majority of identified macroinvertebrate taxa were predators and detritivores, with a small percentage of herbivores. An average of approximately 26% of the macroinvertebrate taxa found were from families that include species from more than one functional feeding group. Although overall measures of diversity and ecosystem health (Fisher’s α and Simpson’s index) remained constant over time in the New Years River, significant differences in macroinvertebrate community structure were seen between sites and months on both rivers, with dissimilarity being driven by a larger number of species in the New Years River. This high variability within macroinvertebrate assemblages probably reflects a combination of heterogeneous duckweed distribution, variation in physico-chemistry, opportunistic behaviours of macroinvertebrate predators and/or successional colonisation of duckweed mats.     

Perceptions towards Egyptian Geese at the Steenberg Golf Estate,Cape Town,South Africa

The number of Egyptian Geese Alopochen aegyptiaca has increased in the Western Cape province, South Africa, during the past few decades and they are allegedly perceived as a problem on golf courses. However, attitudes towards the geese on golf courses in the province have not been empirically assessed. We surveyed the residents and members of the Steenberg Golf Estate, Cape Town, during April 2012 to evaluate perceptions towards Egyptian Geese on the estate. A standardised, anonymous questionnaire was sent to 548 estate residents and non-resident golfing members. Of the 112 respondents, the majority (92, or 84%) considered that geese are a problem on the estate. The ranking of the perceived problem was: 16 (15%) minimal problem, 34 (33%) moderate problem and 54 (52%) severe problem. The majority also considered that the goose population should be reduced by 50% or more (90, or 86% of all respondents). Dealing with Egyptian Geese numbers and activities on golf courses is complex. The option of designing golf courses and adjacent vegetation so that they are attractive to local bird species, while simultaneously being less attractive to Egyptian Geese, is available.     

The dinoflagellate Alexandrium minutum in Cape Town harbour (South Africa): Bloom characteristics, phylogenetic analysis and toxin composition

A novel bloom of Alexandrium minutum occurred in an inner basin of the Cape Town harbour from November 2003 to February 2004. Cellular concentrations reached a maximum of 1.4 × 10⁸ cells l⁻¹ during the mid-December period with corresponding chlorophyll a concentrations of 243 mg m⁻³. Primary productivity measurements conducted during the latter part of the bloom revealed a maximum assimilation number of 11.17 mg C mg Chl a⁻¹ h⁻¹ during the middle of the day. Productivity during this post-peak period was sustained largely by the reduced nitrogen species NH₄ and urea (96%) as measured using ¹⁵N tracer techniques. The large subunit ribosomal DNA sequence of A. minutum isolates from Cape Town harbour was identical to conspecifics collected in Western Europe and in Australia. The composition of tetrahydropurine neurotoxins associated with paralytic shellfish poisoning (PSP) was limited to gonyautoxins (GTX1-GTX4). This profile combined with evidence of a low toxin cell quota (1.5 fmol GTX cell⁻¹) supports a close association of this taxon with other members of the A. minutum species complex, particularly from Europe. Toxin analysis from black mussels collected during this bloom indicated that the accumulated PSP toxins originated from A. minutum and not from Alexandrium catenella as is most often the case along the South African coast.     

A Cross Sectional Analysis of Gonococcal and Chlamydial Infections among Men-Who-Have-Sex-with-Men in Cape Town,South Africa

Background

Men-who-have-sex-with-men (MSM) are at high risk of HIV and sexually transmitted infection (STI) transmission. Asymptomatic STIs are common in MSM and remain undiagnosed and untreated where syndromic management is advocated. Untreated STIs could be contributing to high HIV rates. This study investigated symptomatic (SSTI) and asymptomatic STIs (ASTIs) in MSM in Cape Town.

Methods

MSM, 18 years and above, were enrolled into this study. Participants underwent clinical and microbiological screening for STIs. Urine, oro-pharyngeal and anal swab specimens were collected for STI analysis, and blood for HIV and syphilis screening. A psychosocial and sexual questionnaire was completed. STI specimens were analysed for Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) infection.

Results

200 MSM were recruited with a median age of 32 years (IQR 26–39.5). Their median number of sex partners within the last year was 5 (IQR 2–20). 155/200 (78%) reported only male sex partners while 45/200 (23%) reported sex with men and women. 77/200 (39%) reported transactional sex. At enrolment, 88/200 (44%) were HIV positive and 8/112 (7%) initially HIV-negative participants seroconverted during the study. Overall, 47/200 (24%) screened positive for either NG or CT. There were 32 MSM (16%) infected with NG and 7 (3.5%) of these men had NG infections at two anatomical sites (39 NG positive results in total). Likewise, there were 23 MSM (12%) infected with CT and all these men had infections at only one site. Eight of the 47 men (17%) were infected with both NG and CT. ASTI was more common than SSTI irrespective of anatomical site, 38 /200 (19%) versus 9/200 (5%) respectively (p<0.001). The anus was most commonly affected, followed by the oro-pharynx and then urethra. Asymptomatic infection was associated with transgender identity (OR 4.09 CI 1.60–5.62), ≥5 male sex partners in the last year (OR 2.50 CI 1.16–5.62) and transactional sex (OR 2.33 CI 1.13–4.79) but not with HIV infection.

Conclusions

Asymptomatic STI was common and would not have been detected using a syndromic management approach. Although molecular screening for NG/CT is costly, in our study only four MSM needed to be screened to detect one case. This supports dual NG/CT molecular screening for MSM, which, in the case of confirmed NG infections, may trigger further culture-based investigations to determine gonococcal antimicrobial susceptibility in the current era of multi-drug resistant gonorrhoea.     

Antibiotic resistance and adhesion potential of Bacteroides fragilis clinical isolates from Cape Town, South Africa

The minimum inhibitory concentrations of 23 Bacteroides fragilis clinical isolates from Cape Town, South Africa, were established using the E-test method. Eight percent of the strains were found to be highly resistant to metronidazole (≥256 mg/L) imipenem and cefoxitin. This is an 8% increase in resistance compared to the previous metronidazole susceptibility screening performed in South Africa in 1998. Clindamycin was the most effective antibiotic with all strains showing sensitivity. Most of the strains (65%) were tetracycline resistant, while one strain, B. fragilis GSH15, showed multidrug resistance to metronidazole, imipenem, cefoxitin and tetracycline. PCR screening revealed that none of the strains contained any of the published nim genes. The particle agglutination assay was employed to determine the ability of the isolates to bind the ECM components fibronectin, laminin, mucin and collagen. This revealed that 78% of the clinical isolates adhered to all four ECM components to varying extents, with the strongest being to laminin and weakest to mucin and collagen Type I.     

A contribution to the moss flora of the Cape Provinces (South Africa)

Abstract

Several first records of mosses are reported for continental sub-Saharan Africa, Southern Africa or the Cape Provinces as well as the occurrence of subterranean tuberous stolons in Pleuridium ecklonii and rhizoidal tubers in four acrocarpous mosses, viz. Archidium globiferum, Ditrichum difficile, Fissidens beckettii and Pleuridium nervosum.     

Effectiveness of Patient Adherence Groups as a Model of Care for Stable Patients on Antiretroviral Therapy in Khayelitsha,Cape Town,South Africa

Background

Innovative models of care are required to cope with the ever-increasing number of patients on antiretroviral therapy in the most affected countries. This study, in Khayelitsha, South Africa, evaluates the effectiveness of a group-based model of care run predominantly by non-clinical staff in retaining patients in care and maintaining adherence.

Methods and Findings

Participation in “adherence clubs” was offered to adults who had been on ART for at least 18 months, had a current CD4 count >200 cells/ml and were virologically suppressed. Embedded in an ongoing cohort study, we compared loss to care and virologic rebound in patients receiving the intervention with patients attending routine nurse-led care from November 2007 to February 2011. We used inverse probability weighting to estimate the intention-to-treat effect of adherence club participation, adjusted for measured baseline and time-varying confounders. The principal outcome was the combination of death or loss to follow-up. The secondary outcome was virologic rebound in patients who were virologically suppressed at study entry. Of 2829 patients on ART for >18 months with a CD4 count above 200 cells/µl, 502 accepted club participation. At the end of the study, 97% of club patients remained in care compared with 85% of other patients. In adjusted analyses club participation reduced loss-to-care by 57% (hazard ratio [HR] 0.43, 95% CI = 0.21–0.91) and virologic rebound in patients who were initially suppressed by 67% (HR 0.33, 95% CI = 0.16–0.67).

Discussion

Patient adherence groups were found to be an effective model for improving retention and documented virologic suppression for stable patients in long term ART care. Out-of-clinic group-based models facilitated by non-clinical staff are a promising approach to assist in the long-term management of people on ART in high burden low or middle-income settings.     

Floristic diversity in the Cape Flora of South Africa

Comprising a land area of ca 90000 km2, less than 4% of the total land area for the Southern African subcontinent, the Cape Floristic Province is one of the world's richest areas in terms of botanical diversity for its size. An estimated 8650 species of vascular plants occur in this area, about 65% of which are endemic. This is about 42% of the estimated total for all of southern Africa. The number of species packed into so small an area is remarkable for the temperate zone, and compares closely with species totals for areas of comparable size in the wet tropics. The Cape Region consists of a mosaic of sandstone and shale substrates that give rise to soils of quite different types, and in addition local areas of limestone add to the edaphic diversity. Climates across the region are extremely variable, and the predominant orographic rainfall pattern ranges from 2000mm locally to less than 100mm, often with extremely steep gradients, the result of a mountainous landscape. The edaphic diversity resulting from a mosaic of different soils is compounded by sharp local gradients in precipitation that creates an unusual number of local habitats. A feature of the some of the soils in the Region is low nutrient levels and many of the plants on such soils have low seed dispersal capabilities, a factor important in explaining the high levels of local endemism. Species richness in the Cape Region is hypothesized to have resulted from the presence of a complex mosaic of diverse habitats and steep ecological gradients against a background of relatively stable climate and geology after the mediterranean climate was established there sometime after the beginning of the Pliocene. A local or ecological mode of speciation may have been more important under these conditions than allopatric speciation.     

Habitat selection by the Cape clawless otter (Aonyx capensis) in rivers in the Western Cape Province, South Africa

We radio‐tracked seven Cape clawless otters (Aonyx capensis) (Schinz, 1821) in two rivers in the Western Cape Province, South Africa, providing data on their habitat selection. Habitat type was investigated at a scale that enabled us to separate the effects of types of riparian vegetation, geomorphology and anthropogenic influences. Otters selected areas with boulders and/or reed beds, which provided high crab density and shelter. Direct observations showed that they used two foraging modes depending on the habitat selected. Otters could select open water within c. 8 m of the shore, dive and surface with or without prey. Otherwise hunting involved them moving into shallow water (c. 0.2 m deep), and walking along the substrate feeling for prey with their forefeet. Disturbed possible prey items were then caught with the forefeet.     

A new species of Brachysiphon (Penaeaceae) from the Southern Cape, South Africa

A new chasmophitic species of Brachysiphon, B. microphyllum from the dry interior mountain ranges of the Southern Cape is described.     

Fractionation,mobility and multivariate statistical evaluation of metals in marine sediments of Cape Town Harbour,South Africa

Abstract

Distribution of possible chemical forms of Al, Si, Sn, Pb, Zn, Fe, Hg, Cd and Cu in marine sediments of Cape Town harbour was investigated using a modified Tessier’s sequential extraction procedure and ICP-MS and ICP-AES for heavy metals determination. The mean fractions for all metals at all locations were: 1.5–7196 mg kg^-1 for Si, 7.79–7266 mg kg^-1 for Al, 161-639 mg kg^-1 for Cu, 19–41978 mg kg^-1 for Fe, 2.83–5864 mg kg^-1 for Zn, 1.45–13.26 mg kg^-1for Cd, 9.87–223 mg kg^-1 for Sn, 11.98-979 mg kg^-1 for Pb and 0.13–5.93 mg kg^-1 for Hg. Si, Al and Zn were mostly associated with Fe–Mn oxides, whereas Sn and Hg were mainly bound to residual and organic matter. Pb existed mainly in the residual and iron/manganese oxide phases while Cd was evenly distributed in all the five phases. The loading plots of heavy metals bound to the various chemical forms, as well as Pearson correlation coefficients, enabled the determination binding relationship. Pb, Sn and Hg exhibited similar binding behaviour which indicated an anthropogenic point source from wastes from the ship maintenance workshop, and the presence of Sn in the organic phase can be identified with the use of anti-fouling paints at the harbour, whereas Al, Fe, Si, Cu and Zn would probably be of natural origin. Lastly Cd probably came from a diffuse pollution sources in the harbour due to its unique binding characteristic. The mobility of heavy metals varied depending on location and the heavy metal type. The mobility of metals followed the order: Si > Zn > Fe > Cu> Al> Cd> Pb > Sn > Hg. The high percentage of Cd and Pb in the bioavailable forms suggested the need to keep close surveillance on these metals because of their high toxicity.     

Perceptions related to breastfeeding and the early introduction of complementary foods amongst migrants in Cape Town,South Africa

Background

Infant feeding recommendations are of health importance, yet the extent to which migrant communities in low- and middle-income countries know or implement these recommendations is poorly understood. This study explores the perspectives of infant feeding amongst cross-border migrants in Cape Town, South Africa.

Methods

Between February and October 2013, semi-structured in-depth interviews (n?=?23) were conducted face-to-face with Congolese, Somali and Zimbabwean mothers living in Cape Town. To assess commonly identified narratives of infant feeding, nine focus group discussions (three with men and six with women) were conducted with migrant Somalis, Congolese, and Zimbabweans.

Results

Three dominant themes framed infant feeding. 1) Pragmatism in feeding choices drove responses to baby’s cues, including cries, sleeping patterns, and weight gain (2). Formula feeding was normative in the South African context, whereas lack of commercial infant milk back home was described in terms of expense (3). Low rates of breastfeeding were explained in terms of work responsibilities including household work and lack of breastmilk supply resulting from stress and poor diet. However, women participants typically did not consider their feeding choices to negatively affect their baby’s health.

Conclusions

The reasons for early introduction of both commercial infant milk and solid foods were complex. Breastfeeding was not prioritized despite an awareness of medical recommendations. Rather than emphasizing specific breastfeeding intentions, participants favoured an approach that reacted to their baby’s perceived changing needs. The practical challenges of breastfeeding described by cross-border migrant women reflect one way in which socio-economic and health inequalities may currently be perpetuated for marginalised populations.

     

Brachymesophalangia V in Hottentot and “Cape Colored” children in Namibia (South West Africa) and South Africa

In order to determine the incidence of Brachymesophalangia V, an inspectional and metrical analysis was made of radiographs of 67 Nama-speaking Hottentots aged 2 to 17.5 years, and 210 Rehoboth Basters (in Namibia) and Cape Colored children (near Cape Town) aged 1.5 to 21 years. None of the children displayed cone-shaped epiphysis or early union, and none showed Brachymesophalangia V. It was confirmed that the incidence of Brachymesophalangia V is considerably higher in Mongoloid populations than in Caucasoid or Negroid groups, including Hottentots.     

Ochthebius (s.str.) capicola (Coleoptera) re-discovered in the Cape Peninsula,South Africa

New distributional records and ecological observations are presented for the Cape endemic hydraenid Ochthebius capicola. Considered extinct on the Cape Peninsula, the species has been re-discovered at two adjacent locations as well as at a new site in Tsitsikamma National Park, Eastern Cape. New species associations are recorded, in conjunction with observations confirming this species' preference for algae-covered rock surfaces in the hypersaline pools of the supralittoral zone. Provisional internationally-endangered status for this species was examined but considered dependent on future data. It was considered likely that the beetle may be insufficiently recorded, due to its atypical habitat requirement. A synopsis of the taxonomic status of this species and Ochthebius rubripes is given. Notes on both species are provided, as well as a record of sympatric occurrence.