Algae soil and water samples, Potchefstroom area, North-West province, South Africa
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ABSTRACT:
PROVIDER: PRJNA680473 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13236771_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR13236772_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR13236773_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR13236774_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR13236775_subreads.fastq.gz | Fastqsanger.gz |
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Project description:Background and aimInfections with Campylobacter species have gained recognition as the most frequent cause of foodborne gastroenteritis globally. Their significance in South Africa is still an area of study interest. This study was, therefore, carried out to determine the occurrence of Campylobacter species in chickens from North West Province of South Africa as well as their antibiotic sensitivity status.Materials and methodsA total of 2400 chicken fecal samples were collected and pooled to a total of 480 samples from five registered active poultry abattoirs in the Ngaka Modiri Molema District of North West Province, South Africa. Polymerase chain reaction (PCR) was used for the detection of Campylobacter spp. targeting the 16S rRNA gene while antibiotic sensitivity was determined using disk diffusion inhibition test.ResultsAfter isolation, a total of 26 samples were confirmed to be harboring Campylobacter jejuni by PCR and sequencing. C. jejuni was found to be the only isolate detected in all the fecal samples tested. The study further demonstrated that C. jejuni infections were highest in the summer season (3%) followed by autumn and winter at 1%, while there were none detected in the spring. The isolated C. jejuni-positive samples on disk diffusion inhibition test displayed resistance to nalidixic acid, tetracycline, erythromycin, and ciprofloxacin at 98%, 80%, 83%, and 21%, respectively.ConclusionC. jejuni isolated in this study is known to cause disease in humans, and thus its occurrence requires application of "One Health" strategy to reduce the spread of this zoonotic pathogen in South Africa.
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Project description:Bovine brucellosis affects food safety, food security and human health in rural communities in the North West Province, South Africa. The World Organisation for Animal Health suggests routine sero-surveillance and vaccination of cattle for control and to prevent zoonotic transmission. Although sero-surveillance and subsidised vaccination have been in place for decades, data from Bojanala have not previously been analysed. The aim of this study was to retrospectively analyse historical data on routine sero-surveillance of bovine brucellosis and state subsidised vaccination, in communal, commercial and dairy cattle in the study area. This was a descriptive, cross-sectional retrospective analysis of records from all adult cows bled by the state veterinary services during routine sero-surveillance for bovine brucellosis, in the Bojanala Region, North West Province, between 2009 and 2013. Fewer communal (N = 11 815) and dairy (N = 6696), than commercial beef (N = 28 251) cows, were tested. Overall herd prevalence (33.33%), differed significantly from individual prevalence (3.18%) in all groups. Communal herds had both the highest herd prevalence (38.8%) and the highest individual prevalence (5.2%). Both herd and individual sero-prevalence were lowest in dairy cattle, possibly because registered dairy herds are routinely tested. Over the 5-year study period, only 24 086 (7.15%) of the 342 500 cows eligible for free vaccination, were vaccinated. The annual number of cattle tested was highly variable. Dairy cattle that were regularly tested had a significantly lower herd and individual prevalence. Herd prevalence would be useful for spatial mapping, whilst individual prevalence could better reflect the risk of zoonotic transmission.
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Project description:Building a successful combination prevention program requires understanding the community's local epidemiological profile, the social community norms that shape vulnerability to HIV and access to care, and the available community resources. We carried out a situational analysis in order to shape a comprehensive HIV prevention program that address local barriers to care at multiple contextual levels in the North West Province of South Africa.The situational analysis was conducted in two sub-districts in 2012 and guided by an adaptation of WHO's Strategic Approach, a predominantly qualitative method, including observation of service delivery points and in-depth interviews and focus groups with local leaders, providers, and community members, in order to recommend context-specific HIV prevention strategies. Analysis began during fieldwork with nightly discussions of findings and continued with coding original textual data from the fieldwork notebooks and a select number of recorded interviews.We conducted over 200 individual and group interviews and gleaned four principal social barriers to HIV prevention and care, including: HIV fatalism, traditional gender norms, HIV-related stigma, and challenges with communication around HIV, all of which fuel the HIV epidemic. At the different levels of response needed to stem the epidemic, we found evidence of national policies and programs that are mitigating the social risk factors but little community-based responses that address social risk factors to HIV.Understanding social and structural barriers to care helped shape our comprehensive HIV prevention program, which address the four 'themes' identified into each component of the program. Activities are underway to engage communities, offer community-based testing in high transmission areas, community stigma reduction, and a positive health, dignity and prevention program for stigma reduction and improve communication skills. The situational analysis process successfully shaped key programmatic decisions and cultivated a deeper collaboration with local stakeholders to support program implementation.
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Project description:With the increasing spread of antimicrobial resistance, there is growing attention to the contribution made by drinking water systems. The potential health impact of two drinking water treatment and distribution systems (A and B) in the North-West Province of South Africa was determined by investigating the water quality and occurrence of antimicrobial-resistant heterotrophic bacteria and genes in the raw and treated water over four seasons. Most of the physicochemical parameters except for electrical conductivity were within permissible limits. Coliform bacteria reduced from raw to potable water except for counts higher than the threshold recorded in Summer and Winter. A total of 203 heterotrophic bacterial isolates were recovered on chromogenic R2A medium and subjected to susceptibility testing to twelve antibiotics. Most of the isolates were resistant to β-lactam antibiotics and Trimethoprim, whereas they were susceptible to Ciprofloxacin, Erythromycin, and Neomycin. The proportions of Cephalothin and Kanamycin-resistant isolates were significantly higher (p < 0.05) after treatment for site A, compared to significantly lower β-lactam, Oxytetracycline, and Trimethoprim-resistant isolates for B. Over 50% of isolates were of high risk, indicating their origin from high antibiotic-use sources. Seventy-one (35%) isolates were multidrug-resistant, out of which the majority (53.5%, n = 38) possessed the strA gene, followed by strB 21 (29.6%), dfrB 13 (18.3%), aadA 11 (15.5%), blaCTX-M 5 (7.0%), and tetA 3 (4.2%). The 16S rRNA gene sequences of the isolates revealed strains belonging to eight bacterial families, some of which are clinically important.
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Project description:Bacterial biofilms have recently gained considerable interest in the food production and medical industries due to their ability to resist destruction by disinfectants and other antimicrobials. Biofilms are extracellular polymer matrices that may enhance the survival of pathogens even when exposed to environmental stress. The effect of incubation temperatures (25°C, 37°C, and 40°C) and Salmonella serotype on biofilm-forming potentials was evaluated. Previously typed Salmonella serotypes (55) isolated from the gut of chickens were accessed for biofilms formation using a standard assay. Salmonella Typhimurium ATCC 14028TM and Salmonella Enteritidis ATCC 13076TM (positive controls), Escherichia coli (internal control) and un-inoculated Luria Bertani (LB) broth (negative control) were used. The isolates formed no biofilm (11.86-13.56%), weak (11.86-45.76%), moderate (18.64-20.34%), strong biofilms (23.73-54.24%) across the various temperatures investigated. Serotypes, Salmonella Heidelberg and Salmonella Weltevreden were the strongest biofilm formers at temperatures (25°C, 37°C, and 40°C, respectively). The potential of a large proportion (80%) of Salmonella serotypes to form biofilms increased with increasing incubation temperatures but decreased at 40°C. Findings indicate that average temperature favours biofilm formation by Salmonella serotypes. However, the influence of incubation temperature on biofilm formation was greater when compared to serotype. A positive correlation exists between Salmonella biofilm formed at 25°C, 37°C and 40°C (p ≥ 0.01). The ability of Salmonella species to form biofilms at 25°C and 37°C suggests that these serotypes may present severe challenges to food-processing and hospital facilities.
| S-EPMC7812364 | biostudies-literature
Project description:BackgroundThe protozoan parasite Toxoplasma gondii causes toxoplasmosis, one of the most prevalent parasitic zoonotic diseases with significant economic and public health implications worldwide. Infection with the parasite has a significant adverse effect on sheep and goat production and can frequently go undetected in the herd, resulting in abortions and weak or dead offspring. Although there are few studies on seroprevalence and risk factors associated with T. gondii infections in livestock in other provinces of South Africa, there is no data in the North West province. Therefore, a cross-sectional study was conducted to investigate the seroprevalence of T. gondii and risk factors associated with exposure in sheep and goats of the North West province of South Africa. Sera from 439 livestock (164 sheep and 285 goats) were collected and analysed for the presence of T. gondii IgG antibodies using indirect ELISA (Enzyme-linked immunosorbent assay). An assessment of potential risk factors in farms associated with seropositivity was also conducted using a structured questionnaire.ResultsOut of the 439 tested sheep and goats, 13.9% (61/439) were positive for IgG antibodies against T. gondii. Sheep and goats had seroprevalences of 19.5% (32/164) and 10.5% (29/275) respectively. In the multivariable logistic regression model, the risk of acquiring T. gondii was significantly higher in the mixed breed [Odds ratio (OR) = 71.07; 95% confidence interval (CI): 266.8-1893.1; p < 0.011)] animals than white dorper sheep and in farms that burn or bury aborted material (OR = 42.04; CI: 179.9-982.5; p = 0.020) compared to those that only burn aborted material. The risk was lower for the farms in Kagisano-Molopo (OR = 0.00; CI: 0.0-25.4; p = 0.015) and Mahikeng (OR = 0.00; CI: 0.0-4.9; p < 0.001) local municipalities than Greater Taung local municipality, and for the animals that drink water from dams (OR = 0.03; CI: 0.2-58.8; p = 0.021) than those that drink from boreholes.ConclusionThe seroprevalence and risk factors associated with transmission observed show that T. gondii infection is widespread in sheep and goats of the North West province.
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