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.     

Activity patterns of springhares from the Eastern Cape Province, South Africa

The activity patterns of springhares Pedetes capensis ( Rodentia: Pedetidae ) from the Eastern Cape Province, South Africa, were investigated by counting the number of springhares active above ground at regular intervals throughout the night at different times of the year and under different weather conditions and phases of the moon. A combination of time of year, time of night and level of illumination best explained springhare activity, accounting for 43% of the variation in springhare numbers. Springhare activity generally reached its peak soon after dark, thereafter remaining fairly constant throughout most of the night and only decreasing in the 2–4-h period before sunrise. On those nights when the moon either rose or set during the night, this pattern was modified by the level of illumination. Springhares responded to moonlight by reducing above-ground activity, shifting activity to dark, moonless periods of the night, and by reducing their use of open space. Except for extremes, other weather conditions had no significant effect on springhare activity.     

Diversity of SCCmec elements in methicillin-resistant coagulase-negative staphylococci clinical isolates

Background

Methicillin-resistant coagulase-negative staphylococci (MR-CoNS) are opportunistic pathogens and serve as a large reservoir of staphylococcal cassette chromosome mec (SCCmec). Characterization of SCCmec in MR-CoNS can generate useful information on the mobilization and evolution of this element.

Methodology/Principal Findings

Non-repetitive MR-CoNS clinical isolates (n = 84; 39 S. epidermidis, 19 S. haemolyticus, 9 S. hominis, 6 S. capitis, 4 S. warneri, 2 S. cohnii, 2 S. saprophyticus, 1 S. kloosii, 1 S. simulans and 1 S. massiliensis) were collected. All isolates could grow on plates with 4 mg/L cefoxitin and all had mecA as detected by PCR. Strain typing using RAPD and ERIC-PCR revealed that almost all isolates were of different strains. SCCmec typing was performed using multiplex PCR published previously. For isolates in which SCCmec could not be typed, the mec complex classes were determined by additional PCR and the ccr genes were amplified with published or newly-designed primers and then sequenced. SCCmec types were assigned for 63 isolates by multiplex PCR and were assigned for 14 other isolates by PCR targeting mec and ccr. Among 77 isolates with determined SCCmec types, 54 had a single type, including type III (n = 19), IV (n = 14), V (n = 10), II (n = 2), I (n = 1), VIII (n = 1) and five unnamed types (n = 7), while 23 isolates had two types, III+V (n = 12), II+V (n = 8), II+IV (n = 2) or IV+V (n = 1). The five unnamed types were assigned UT1 (class A mec, ccrA1/ccrB4), UT2 (class C1 mec, ccrA4/ccrB4), UT3 (class A mec, ccrA5/ccrB3), UT4 (class C2 mec, ccrA2/ccrB2 plus ccrC1) and UT5 (class A mec, ccrA1/ccrB1 plus ccrC1).

Conclusions/Significance

SCCmec types III, IV and V were prevalent in MR-CoNS and many isolates could harbor more than one type. Several new types of SCCmec were identified, highlighting the great genetic diversity and the need of developing classification schemes for SCCmec in MR-CoNS.     

Antibiotic resistance and molecular characterization of clinical isolates of methicillin-resistant coagulase-negative staphylococci isolated from bacteremic patients in oncohematology

Polymerase chain reaction (PCR) amplification of antibiotic resistance genes as well as staphylococcal cassette chromosome mec (SCCmec) typing and pulsed-field gel electrophoresis (PFGE) of SmaI macrorestriction fragments of genomic DNA were used to characterize 45 methicillin-resistant coagulase-negative staphylococci (MRCoNS) isolates responsible of bacteremia recovered in patients at the Bone Marrow Transplant Centre of Tunisia in 1998–2007. Among the 45 MRCoNS isolates, Staphylococcus epidermidis was the most prevalent species (75.6%) followed by Staphylococcus haemolyticus (22.2%) and Staphylococcus hominis (2.2%). Extended susceptibility profiles were generated for MRCoNS against 16 antimicrobial agents. Out of 45 mecA-positive strains, 43 (95.6%) were phenotypically methicillin-resistant and two (4.4%) were methicillin-susceptible. The msr(A) was the most prevalent gene (13 isolates; 48.1%) among erythromycin-resistant isolates. The erm(C) was found alone in seven (25.9%) or in combination with both erm(A) and erm(B) in two (7.4%) isolates. The aac(6′)-Ie-aph(2″)-Ia was the most prevalent gene among aminoglycoside-resistant isolates, detected alone in 14 isolates (33.3%) isolates, in combination with ant(4′)-Ia in 18 (42.8%) isolates, in combination with aph(3′)-IIIa in four (9.5%) or with both ant(4′)-Ia and aph(3′)-IIIa in two (4.7%) isolates. The ant(4′)-Ia was detected in three (7.1%) isolates and the aph(3′)-IIIa in one (2.4%) isolate. Among tetracycline-resistant isolates, six (85.7%) strains harbored the tet(K) gene and one (14.3%) strain carried tet(K) and tet(M) genes. SCCmec types IV (31%) and III (24.5%), the most prevalent types detected, were found to be more resistant to non-β-lactam antibiotics. A wide diversity of isolates was observed by PFGE among MRCoNS.     

Co-trimoxazole resistance in methicillin-resistant staphylococci isolated from clinical material in 2001-2003

The aim of this study was to determine resistance to co-trimoxazole among 476 strains of methicillin-resistant Staphylococus aureus (MRSA) and 2137 strains of methicillin resistant coagulase-negative staphylococci (MRCNS) isolation during three years (2001-2003). Their susceptibility testing were performed by the disc-diffusion techniques according to recomendation of NCCLS (National Committe for Clinical Laboratory Standards). Co-trimoxazole resistance was demonstrated more frequently among MRCNS (52,8%, 51,4%, 63,9% in 2001, 2002, 2003), than among MRSA (23,4%, 19,5%, 16,8% adequately).     

Risk factors of porcine cysticercosis in the Eastern Cape Province, South Africa

There is a high prevalence of Taenia solium taeniosis/cysticercosis in humans and pigs in the Eastern Cape Province (ECP) of South Africa. The objective of this study was to identify risk factors of porcine cysticercosis in select districts of the ECP. Data were collected in 2003 by interviewing 217 pig producers from the area. Blood samples were collected from 261 of their pigs, which were tested using two enzyme-linked immunosorbent assays (ELISA) for the presence of antibodies to cysticercosis. Frequencies of both owner- and pig-level characteristics were determined. For pig-level analysis, all bivariable and multivariable associations were determined using the surveylogistic procedure of the SAS/STAT? software to accommodate for the intraclass correlation that exists for clusters of pigs within one owner and for clusters of owners within a district. All tests for significance were performed at the α?=?0.05 level, and adjusted odds ratios (aOR) and 95% confidence intervals (CI) were determined. Among the respondents, 48% of their households lacked a latrine, 98% slaughtered pigs at home, and 99% indicated that meat inspection services were not available. On bivariable analysis, there was a significant association between porcine infection and district (p?=?0.003), breed (p?=?0.041) and the absence of a latrine (p?=?0.006). On multivariable analysis, the absence of a latrine was the only variable significantly associated with porcine infection (aOR?=?1.89; 95% CI?=?1.07, 3.35) (p?=?0.028). The increased odds of porcine infection with households lacking a latrine contributes to our understanding of the transmission of this parasite in the ECP. Determining and addressing the risk factors for T. solium infection can potentially lower the very high prevalence in humans and pigs in this endemic area.     

The pigments from Pinnacle Point Cave 13B, Western Cape, South Africa

Earth pigments from the three excavations at Pinnacle Point Cave 13B (Western Cape Province, South Africa), spanning the terminal middle Pleistocene and earlier late Pleistocene, are described and analyzed. Qualitative geological categorization primarily rested on textural, fabric, and iron enrichment attributes. Comprehensive recovery allowed identification of non-anthropic pigmentaceous materials, questionable pigments, and 380 pigments (1.08?kg). Less chemically altered pigments were typically fine-grained sedimentary (FGS) rocks, tending to be soft, highly micaceous, prone to laminar fragmentation, and with reddish-brown streaks of intermediate nuance. More iron-enriched forms tended to be harder, denser, poorly micaceous, and with redder streaks of more saturated nuance. Some still qualified as FGS forms, but a large number were categorized as sandstone or iron oxide. Despite some temporal change in raw material profiles, circumstantial evidence suggests primarily local procurement from one outcrop throughout the sequence. Definitely utilized pieces (12.7%) were overwhelmingly ground. Unusual forms of modification include several notched pieces and a deliberately scraped 'chevron.' Controlling for fragmentation, streak properties of utilized versus unutilized pieces were used to investigate selective criteria. There was robust evidence for preferential grinding of the reddest materials, strongly suggestive evidence for saturation and darkness being subordinate selective criteria, and some indication of more intensive grinding of materials with the reddest, most saturated, and darkest streaks, and for some deliberate heating of pigments. These findings challenge the initial stages of color lexicalization predicted by the various versions of the basic color term (BCT) hypothesis, they provide grounds for rejecting hafting as a general explanatory hypothesis, and they cannot be accounted for by incidental heating. The results are more consistent with agreed upon canons of ornamentation than with individual display. It is concluded that the material was processed to produce saturated red pigment powders. On theoretical grounds, these are presumed to have served primarily as body paints in ritual performance.     

Evidence for prey selection by spotted hyaena in the Eastern Cape,South Africa

We tested the widely accepted hypothesis that spotted hyaenas (Crocuta crocuta) are non-selective in their diet. The prey preference of spotted hyaena was studied in the Addo Elephant National Park (AENP), South Africa. Diet (frequency of occurrence of prey items in the diet) was quantified through the analysis of 55 scats, and compared with available prey. A combination of large- and medium-sized mammals (buffalo (Syncerus caffer), red hartebeest (Alcelaphus buselaphus) and common duiker (Sylvicapra grimmia) were the most preferred prey items. The most abundant species, warthog (Phacochoerus africanus) and kudu (Tragelaphus strepsiceros), were ignored and avoided, respectively. These results show that the assumption that hyaena prey on the most abundant available prey species may be overly simplistic. Predation patterns, such as the ones observed in AENP, may have important ramifications for less common species that are selected by hyaena in small enclosed reserves.     

Age and population group related distribution of enteropathogens in the Eastern Cape, South Africa

The frequency of Salmonella spp., Shigella spp., Campylobacter spp., Yersinia enterocolitica, Aeromonas hydrophilia and Helminths in samples from various hospitals of the Eastern Cape, South Africa, were analysed for trends involving age distribution and population group. Significant differences in the distribution of these pathogens could be attributed to hygiene and environmental difference between the age and population groups which suggests that rapid urbanization and poor water supply remain major problems in the drought prone Eastern Cape.     

Transformation of thicket to savanna reduces soil quality in the Eastern Cape, South Africa

Xeric succulent thicket in the Eastern Cape, South Africa has been used for farming goats since the early 1900s. This habitat is characterised by a dense cover of the succulent bush Portulacaria afra and by a warm, semi-arid climate with evenly distributed annual rainfall of 250–400 mm. Heavy browsing by goats results in the loss of P. afra and transforms the thicket to an open savanna dominated by annual grasses. Eight fence-line comparisons between thicket and savanna were used to investigate differences in soil quality associated with the vegetation change. Composite soil samples were taken to a depth of 10 cm from 1 ha plots on either side of the fence-line. Associated with the change from thicket to savanna, a significant decrease (paired t-test, P < 0.05) was found in total C (respective means of 5.6 vs. 3.0%), total N (0.33 vs. 0.24%), labile C (2.8 vs. 1.5%), CO₂ flux (1.9 vs. 0.5 µmol m^–2 s^–1), soil respiration in the laboratory (144 vs. 79 ng C kg^–1 s^–1), (NH₄)OAc-extractable Mg (55 vs. 28 mmol_c kg^–1), and laboratory infiltration rate (51 vs. 19 mm h^–1). In the same direction there was a similarly significant increase in modulus of rupture (16 vs. 34 kPa), water-soluble Ca (2.3 vs. 3.4 mmol_c kg^–1) and pH (6.7 vs. 7.7). The soil C content of 5.6% in thicket is surprisingly high in this warm, semi-arid climate and suggests that the dense P. afra bush strongly regulates soil organic matter through microclimate, erosion control, litter quantity and perhaps chemistry. Savanna soils had a greater tendency to crust (as evident in a lower rate of laboratory infiltration and greater modulus of rupture) than thicket soils. This was attributed to their lower organic matter content, which probably reduced aggregate stability. Savannas are likely to be more prone to runoff and erosion not only because of sparser vegetation but also because of a decline in soil quality.     

Patterns of chironomid body-size distribution in an effluent-impacted river in the Eastern Cape,South Africa

Body size is an important determinant of assemblage structure in rivers and streams impacted by elevated concentrations of pollutants such as salts and metals. In the present study, because of the larger surface-area-tovolume ratio of small-bodied chironomid species compared with large-bodied species, it was hypothesised that the relative abundance of the small-bodied species would decrease at the impacted sites by elevated concentrations of total dissolved solids compared with that at the less-impacted control site. The aim of this study was to analyse and compare patterns of chironomid final instar body-size classes at impacted sites with those at the control site. Chironomid larvae were sampled seasonally from August 2009 to September 2012 from one control site and three impacted sites (Sites 2, 3 and 4) in the Swartkops River, Eastern Cape. Site 2 was impacted by diffuse pollution sources, whereas Sites 3 and 4 were impacted by wastewater effluent discharges in addition to diffuse pollution sources. Small-bodied species dominated the assemblage at the control site and declined significantly at the impacted sites, suggesting that chironomid body size responds predictably to deteriorating water quality in the Swartkops River.     

The spawning behaviour of the endangered Eastern Cape rocky, Sandelia bainsii (Anabantidae), in South Africa

Sandelia bainsii is an endangered freshwater fish species which only occurs in short sections of several Eastern Cape river systems in South Africa. The spawning behaviour of S. bainsii is described for the first time. Female S. bainsii remained a light grey colour. Males exhibited distinctive nuptial coloration consisting of an intense black with a white bar on their caudal fin and white windows on the posterior areas of their dorsal and anal fins. There was a darkened post orbital contact organ of ctenoid scales on the reproductively active males. The spawning behaviour was recorded on a video recorder and analyzed during frame by frame replay. Sandelia bainsii are uniparental substrate breeders. The male prepared a spawning area by clearing the substrate with rapid body movements (sweeps). There were a number of preliminary courtship movements, several trial embraces by the male before the actual final embrace. The male underwent a U bend around the female, anchored himself with the contact organ, squeezed the abdominal area of the female with a quick head movement. Courtship and spawning all took place near the substratum. Twenty one separate mating bouts were filmed and analyzed. The duration varied from 1.44 to 5.11 seconds with an average embrace of 3.39 seconds. During the mating clench the female was not normally turned over, as in some anabantoids, but remained upright. The male then guarded the spawning area. Eggs were light yellow, adhesive, demersal and 1.28 mm in diameter with 0.61 mm oil globules. The breeding behaviour of S. bainsii has some similarities with both breeding behaviourial groups, the bubble nesters and the free spawners, within the other African anabantid genus, Ctenopoma. Sandelia bainsii have acquired some temperate specializations with regard to their reproductive style. Free spawning and the release of buoyant eggs is the plesiomorphic anabantid reproductive style. The demersal eggs and male substratum nest sites of S. bainsii are considered apomorphic.     

Apparent range expansion of the Redbilled Quelea Quelea quelea in the Eastern Cape Province of South Africa

Whittington-Jones, C.A. 1997. Apparent range expansion of the Redbilled Quelea Quelea quelea in the Eastern Cape Province of South Africa. Ostrich 68 (2–4): 97–103.

Distribution records obtained from the South African Bird Atlas Project (SABAP) and from published literature show that the known distribution of Redbilled Quelea in the Eastern Cape has changed dramatically over the last century. Increased search effort following the initiation of SABAP may explain the range expansion, but changes in agricultural practice have probably been a contributing factor.     

The distribution and state of mangroves along the coast of Transkei,Eastern Cape Province,South Africa

The mangrove communities along the coastline of the former Transkei, now part of the Eastern Cape Province, have not been looked at in detail since Ward and Steinkes survey in 1982. Mangroves previously occurred in 17 estuaries but were now found in only 14 of the 76 estuaries visited, with a complete loss of mangroves evident in the Mnyameni, Mzimvubu and Bulungula estuaries amounting to 7.5 ha. Total mangrove loss amounted to 17.6 ha which represents a 6.5% loss over 17 years or 1.04 ha per annum. Tree cover had increased by 16.15 ha in eight other estuaries. This increase could be attributed to the inaccessibility of mangrove stands or to protection afforded by provincial nature reserves and hotel resorts. No new mangrove stands were recorded, although Steinke (pers. comm.) has recently recorded mangroves along the north bank of the Kei River. There has been little change in mangrove species composition in the different estuaries over the past 17 years. Total mangrove loss amounted to 17.6 ha which represents a 6.5% loss over 17 years or 1.04 ha per annum and the species recorded included Avicennia marina, Bruguiera gymnorhiza and Rhizophora mucronata. The mangrove fern Acrostichum aureum L. was recorded for the first time in the Mkozi estuary. Tree density for all estuaries was between 10 and 2594 trees ha^–1. The Mngazana and Mntafufu estuaries had the highest tree densities of 2594 and 1402 trees ha^–1 respectively, typical of riverine mangrove forests. Fringe mangroves were evident in most other systems. Removal of trees for wood has the greatest impact on mangrove cover. Fringe mangrove stands are particularly accessible to harvesters. Only 6% of the current area of trees is afforded some protection in conservation areas. The Mdumbi, Mzamba and Kobonqaba estuaries receive no conservation protection and harvesting has resulted in more than 50% of the trees being removed. The density of dead tree stumps was greater than the number of living trees and no seedlings or juvenile trees were found. Further removal of mangroves within the estuaries south of the Mzimvubu River is expected in the fringe mangroves, as most are unprotected and easily accessible.     

Detection of Transgenes in Local Maize Varieties of Small-Scale Farmers in Eastern Cape,South Africa

Small-scale subsistence farmers in South Africa have been introduced to genetically modified (GM) crops for more than a decade. Little is known about i) the extent of transgene introgression into locally recycled seed, ii) what short and long-term ecological and socioeconomic impacts such mixing of seeds might have, iii) how the farmers perceive GM crops, and iv) to what degree approval conditions are followed and controlled. This study conducted in the Eastern Cape, South Africa, aims primarily at addressing the first of these issues. We analysed for transgenes in 796 individual maize plants (leaves) and 20 seed batches collected in a village where GM insect resistant maize was previously promoted and grown as part of an governmental agricultural development program over a seven year period (2001–2008). Additionally, we surveyed the varieties of maize grown and the farmers’ practices of recycling and sharing of seed in the same community (26 farmers were interviewed). Recycling and sharing of seeds were common in the community and may contribute to spread and persistence of transgenes in maize on a local or regional level. By analysing DNA we found that the commonly used transgene promoter p35s occurred in one of the 796 leaf samples (0.0013%) and in five of the 20 seed samples (25%). Three of the 20 seed samples (15%) included herbicide tolerant maize (NK603) intentionally grown by the farmers from seed bought from local seed retailers or acquired through a currently running agricultural development program. The two remaining positive seed samples (10%) included genes for insect resistance (from MON810). In both cases the farmers were unaware of the transgenes present. In conclusion, we demonstrate that transgenes are mixed into seed storages of small-scale farming communities where recycling and sharing of seeds are common, i.e. spread beyond the control of the formal seed system.     

Occurrence of macrolide-lincosamide-streptogramin B resistant isolates of Staphylococcus aureus in clinical specimens in 2003-2004

The aim of the study was the analysis of frequency of macrolide-lincosamide-streptogramin B (MLS(B)) resistance among MSSA (n=1682) and MRSA (n=272) strains which were isolated in 2002-2004 from various clinical materials from patients hospitalized in the University Hospital at the L. Rydygier Collegium Medicum in Bydgoszcz, University of Nicolaus Copernicus in Toruń. Susceptibility testing and examination of methicillin-resistant strains were performed by the disc diffusion techniques according to recommendation of NCCLS. Resistance to the MLS(B) antimicrobials agents was higher among MRSA compared to MSSA isolates. The MLS, constitutive phenotype was more prevalent than the MLS(B) inducible phenotype among investigated MRSA (65.4%) and MSSA (7.6%) isolates. Inducible resistance had only 2.5% of the MSSA and 2.6% of the MRSA strains. Moreover in 2004 there were found increasing frequency of inducible MLS(B) resistance from 1.1% to 5.7% and decreasing frequency of constitutive MLS(B) resistance from 9.2% to 4.7% among MSSA strains, in comparison to 2003. The investigated MSSA MLS(B)-, MLS(B)- and MRSAMLS(B)+, MLS(B)- strains were the most frequently isolated from pus (adequately 5.2%, 28.8% and 30.5%, 10.7%) and also from nosopharynx swabs (1.7% MSSA MLS(B)+ and 22.9% MSSA MLS(B)-) and biomaterials (15,1% MRSA MLS(B)+ and 9.6% MRSA MLS(B)-). They mainly came from patients of the outpatient clinic (2,4% MSSA MLS(B)+ and 19.9% MSSA MLS(B)-) and patients treated at the neurosurgical ward (20.6% MRSA MLS(B)+ and 12.1% MRSA MLS(B)-).