Pathogen In South Africa Research Articles

First Report of Fusarium Wilt and Pink Rot of Phoenix canariensis in South Africa

ABSTRACTCanary Island date palm, Phoenix canariensis, is a popular ornamental species commonly planted in urban areas worldwide, including South Africa. In November 2023, symptoms typical of Fusarium wilt were detected on ornamental palms at the Waterfront in Cape Town, Western Cape Province, South Africa. Samples were collected from three wilting palms with one‐sided frond death and pink sporulation on the bark. Isolations to culture media yielded two fungal species, which were confirmed based on DNA sequence data as Fusarium oxysporum f.sp. canariensis (Foc) and Nalanthamala vermoesenii. Fusarium wilt, caused by Foc, is among the most serious diseases of these palms. There is no effective treatment for this vascular wilt disease and infected palms inevitably die. Pink rot, caused by N. vermoesenii, is commonly found as a secondary infection associated with Fusarium wilt in P. canariensis. This is the first detection of the Fusarium wilt and pink rot pathogens in South Africa.

Whole Genome Sequence Analysis of Brucella spp. from Human, Livestock, and Wildlife in South Africa

Brucellosis is an economically important zoonotic disease affecting humans, livestock, and wildlife health globally and especially in Africa. Brucella abortus and B. melitensis have been isolated from human, livestock (cattle and goat), and wildlife (sable) in South Africa (SA) but with little knowledge of the population genomic structure of this pathogen in SA. As whole genome sequencing can assist to differentiate and trace the origin of outbreaks of Brucella spp. strains, the whole genomes of retrospective isolates (n = 19) from previous studies were sequenced. Sequences were analysed using average nucleotide identity (ANI), pangenomics, and whole genome single nucleotide polymorphism (wgSNP) to trace the geographical origin of cases of brucellosis circulating in human, cattle, goats, and sable from different provinces in SA. Pangenomics analysis of B. melitensis (n = 69) and B. abortus (n = 56) was conducted with 19 strains that included B. abortus from cattle (n = 3) and B. melitensis from a human (n = 1), cattle (n = 1), goat (n = 1), Rev1 vaccine strain (n = 1), and sable (n = 12). Pangenomics analysis of B. melitensis genomes, highlighted shared genes, that include 10 hypothetical proteins and genes that encodes for acetyl-coenzyme A synthetase (acs), and acylamidase (aam) amongst the sable genomes. The wgSNP analysis confirmed the B. melitensis isolated from human was more closely related to the goat from the Western Cape Province from the same outbreak than the B. melitensis cattle sample from different cases in the Gauteng Province. The B. melitensis sable strains could be distinguished from the African lineage, constituting their own African sub-clade. The sequenced B. abortus strains clustered in the C2 lineage that is closely related to the isolates from Mozambique and Zimbabwe. This study identified genetically diverse Brucella spp. among various hosts in SA. This study expands the limited known knowledge regarding the presence of B. melitensis in livestock and humans in SA, further building a foundation for future research on the distribution of the Brucella spp. worldwide and its evolutionary background.

Whole genome molecular analysis of respiratory syncytial virus pre and during the COVID-19 pandemic in Free State province, South Africa

Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The Coronavirus disease 2019 (COVID-19) pandemic and resulting nonpharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South Africa. A seasonality shift and RSV resurgence was observed in 2020 and 2021, with several infected children observed. Conventional RSV-positive nasopharyngeal swabs were collected from various hospitals in the Free State province, Bloemfontein, South Africa, from children suffering from respiratory distress and severe acute respiratory infection between 2020 to 2021. Overlapping genome fragments were amplified and complete genomes were sequenced using the Illumina MiSeq platform. Maximum likelihood phylogenetic and evolutionary analysis were performed on both RSV-A/-B G-genes with published reference sequences from GISAID and GenBank. Our study strains belonged to the RSV-A GA2.3.2 and RSV-B GB5.0.5a clades. The upsurge of RSV was due to pre-existing strains that predominated in South Africa and circulating globally also driving these off-season RSV outbreaks during the COVID-19 pandemic. The variants responsible for the resurgence were phylogenetically related to pre-pandemic strains and could have contributed to the immune debt resulting from pandemic imposed restrictions. The deviation of the RSV season from the usual pattern affected by the COVID-19 pandemic highlights the need for ongoing genomic surveillance and the identification of genetic variants to prevent unforeseen outbreaks in the future.

Collaborative research on influenza and other respiratory pathogens in South Africa (CDC)

Collaborative research on influenza and other respiratory pathogens in South Africa (CDC)

The first report of Phytophthora multivesiculata causing black rot of Cymbidium and Ansellia africana from South Africa.

Globally, various species and hybrids of Cymbidium are of horticultural importance. In January 2022, we visited a private orchidarium near Pretoria (25° 54' 30" S, 28° 24' 34" E). During this visit, the owner reported mortality among various pure and hybrid Cymbidium and Ansellia africana, an indigenous South African ornamental orchid. Phytophthora was identified as a possible causative agent based on an initial examination of the affected orchids. The infected orchids exhibited vascular wilting. Brown, water-soaked lesions covered the roots. The pseudobulbs showed black rot symptoms. Necrotic lesions were also visible towards the basal part of the leaves. For isolation of the causal agent, pieces of infected tissues from roots, pseudobulbs and leaves were surface sterilised using 70% ethanol and plated into Phytophthora selective medium, NARPH. All the plates were incubated at 21°C in darkness. After three days, Phytophthora-like mycelia emerged from all three tissue types. These colonies were transferred onto the PDA medium. For molecular identification, genomic DNA was extracted from four representative isolates (CMW58027-30) using a Zymo Research Fungal/Bacterial DNA MiniPrep kit. The complete ITS, and partial beta-tubulin (BT) and cytochrome oxidase 1 (COX1) gene regions were amplified using the primers DC6/ITS4 (Cooke et al. 2000; White et al. 1990), Btub_F1A/Btub_R1 (Blair et al. 2008; Kroon et al. 2004) and FM84/FM83 (Martin and Tooley 2003), respectively. BLAST searches in NCBI showed that the four isolates were from Phytophthora ITS Clades 2. ITS, BT, and COX1 datasets from Bose et al. (2021) were used for the phylogenetic identification of our isolates. Single gene and concatenated datasets were analysed using both maximum likelihood and Bayesian approaches, which confirmed the identity of the isolates as Phytophthora multivesiculata. All the sequences were submitted to the GenBank: ITS (OM967212-15), BT (OM966588-91), and COX1 (OM966592-95). Measurements of sporangia and gametangia overlapped with those from Ilieva et al. (1998): sporangia (28.3 - 56.3) 41.6 x 31.3 (21.5 -3 9.6) µm; L:B 1.42 (1.08 - 1.69); exit pore 11.2 (7.1 - 14.6) µm; oogonia 44.2 (24.5 - 56.3) µm; oospore 34.2 (21.6 - 53.2) µm; antheridia (5.8 - 14.6) 11.8 x 15.3 (6.2-14.9) µm. The pathogenicity trial was conducted following the protocol suggested by Ilieva et al. (1998). Five A. africana roots and the cut ends of seven Cymbidium leaves were immersed in separate beakers containing 100 ml of sterile distilled water and ten 5 mm agar discs excised from a 7-day-old culture of P. multivesiculata (CMW58027) grown on PDA. Sterile distilled water was used as the control, with an equal number of plants and leaves. All of the sets were incubated at 21°C. After seven days, the plants and leaves developed lesions similar to those observed on the symptomatic plants at the orchidarium. Trials were repeated once and the pathogen was reisolated from both trials and the identity was confirmed by amplifying the complete ITS gene region. Phytophthora multivesiculata has been previously reported from the Netherlands (Ilieva et al. 1998), Taiwan (Chern et al. 2011), Australia (Cunnington et al. 2009), New Zealand (Hill 2004) and elsewhere causing black rot of Cymbidium. However, this is the first report of P. multivesiculata causing black rot of Cymbidium and A. africana from Africa. We are now conducting follow-up surveys to determine the distribution range of this pathogen in South Africa.

S8.1b Is a search and destroy strategy still feasible for Candida auris in South Africa?

S8.1 Tackling Candida auris in resource-limited settings, September 23, 2022, 3:00 PM - 4:30 PM Candida auris was prospectively detected as a healthcare-associated pathogen in South Africa in 2014. However, a retrospective review of a culture collection from national laboratory-based surveillance for Candidaemia in 2009-10 showed that earlier cases had been missed owing to species misidentification. National surveillance, which was repeated during 2016-17, revealed that C. auris caused >10% of cases of Candidaemia in South Africa, with most (86%) cases detected in the Gauteng Province. We recommended all hospitals to passively monitor cases of C. auris disease and colonization by each maintaining a line list of culture-confirmed cases. Facilities were thus classified into three tiers. Tier 1 (‘green status’) included facilities with no prior known cases. Such facilities were requested to report their first cases for urgent intervention. This included active colonization surveys, isolation and/or cohorts of infected or colonized patients as well as intensified infection prevention and control and antifungal stewardship activities. Tier 2 (‘orange status’) included facilities with sporadic cases defined arbitrarily as fewer than 12 cases in the past 6 months and/or fewer than three units affected. Such facilities were requested to report any increase in the number of cases compared with a baseline, clinical units affected for the first time, or apparent case clustering within the facility for investigation. Tier 3 (‘red status’) included facilities with a relative endemicity defined as >12 cases and/or >3 units with cases in the last 6 months. Tier 3 facilities were only requested to report increases over a baseline or apparent clustering within the facility. Owing to limited resources, colonization screening of newly-admitted patients was not recommended in acute-care facilities in South Africa. During 2019-21, the proportion attributable to C. auris increased even further to 25% (of 12 959 national cases of Candidaemia), with a concomitant reduction in cases caused by C. parapsilosis. This suggested a concerning replacement of multidrug-resistant C. auris in an ecological healthcare niche previously occupied by azole-resistant C. parapsilosis. An epidemiological shift was also observed with an expanding number of acute healthcare facilities outside Gauteng Province reporting C. auris and large persistent healthcare-associated infection outbreaks in neonatal units, particularly in the under-resourced public health sector.

A serious shoot and leaf disease caused by Colletotrichum theobromicola discovered on eucalypts in South Africa

Eucalypt plantations in South Africa make up an important part of the local forestry industry. Recently, one-year-old nursery plants of a Eucalyptus grandis × Eucalyptus urophylla variety displayed symptoms of leaf and shoot anthracnose disease. Samples were collected from these plants and isolations were made from the disease symptoms. Isolates were identified based on their morphological characteristics and DNA sequence data for eight gene regions. Phylogenetic analyses led to the isolates being identified as Colletotrichum theobromicola and the reduction of Colletotrichum pseudotheobromicola to synonymy with the former species. Pathogenicity trials with isolates of C. theobromicola were conducted on clones of E. grandis and hybrids of E. grandis × E. urophylla and E. grandis × Eucalyptus camaldulensis. Resulting symptoms were similar to those found on naturally infected plants and the fungus was re-isolated from the infections. Colletotrichum theobromicola is known to cause anthracnose on various plants including eucalypts in Brazil, but this is the first record of the pathogen in South Africa.

Pathogenicity Testing of Fungal Isolates Associated with Olive Trunk Diseases in South Africa.

A recent olive trunk disease survey performed in the Western Cape Province, South Africa, identified several fungi associated with olive trunk disease symptoms, including species of Basidiomycota, Botryosphaeriaceae, Coniochaetaceae, Calosphaeriaceae, Diaporthaceae, Diatrypaceae, Phaeomoniellaceae, Phaeosphaeriaceae, Symbiotaphrinaceae, Togniniaceae, and Valsaceae. Many of the species recovered had not yet been reported from olive trees; therefore, the aim of this study was to determine their pathogenicity toward this host. Pathogenicity tests were first conducted on detached shoots to select virulent isolates, which were then used in field trials. During field trials, 2-year-old olive branches of 15-year-old trees were inoculated by inserting colonized agar plugs into artificially wounded tissue. Measurements were made of the internal lesions after 8 months. In total, 58 isolates were selected for the field trials. Species that formed lesions significantly larger than the control could be considered as olive trunk pathogens. These included Biscogniauxia rosacearum, Celerioriella umnquma, Coniochaeta velutina, Coniothyrium ferrarisianum, isolates of the Cytospora pruinosa complex, Didymocyrtis banksiae, Diaporthe foeniculina, Eutypa lata, Fomitiporella viticola, Neofusicoccum stellenboschiana, Neofusicoccum vitifusiforme, Neophaeomoniella niveniae, Phaeoacremonium africanum, Phaeoacremonium minimum, Phaeoacremonium oleae, Phaeoacremonium parasiticum, Phaeoacremonium prunicola, Phaeoacremonium scolyti, Phaeoacremonium spadicum, Pleurostoma richardsiae, Pseudophaeomoniella globosa, Punctularia atropurpurascens, Vredendaliella oleae, an undescribed Cytospora sp., Geosmithia sp., two undescribed Neofusicoccum spp., and four Xenocylindrosporium spp. Pseudophaeomoniella globosa can be regarded as one of the main olive trunk pathogens in South Africa because of its high incidence from olive trunk disease symptoms in established orchards and its high virulence in pathogenicity trials.

Isolation and antibiotic sensitivity of Campylobacter species from fecal samples of broiler chickens in North West Province, South Africa.

Background and Aim:Infections 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 Methods:A 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.Results:After 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.Conclusion:C. 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.

Genomic Insights of Multidrug-Resistant Escherichia coli From Wastewater Sources and Their Association With Clinical Pathogens in South Africa.

There is limited information on the comparative genomic diversity of antibiotic-resistant Escherichia coli from wastewater. We sought to characterize environmental E. coli isolates belonging to various pathotypes obtained from a wastewater treatment plant (WWTP) and its receiving waters using whole-genome sequencing (WGS) and an array of bioinformatics tools to elucidate the resistomes, virulomes, mobilomes, clonality, and phylogenies. Twelve multidrug-resistant (MDR) diarrheagenic E. coli isolates were obtained from the final effluent of a WWTP, and the receiving river upstream and downstream of the WWTP were sequenced on an Illumina MiSeq machine. The multilocus sequence typing (MLST) analysis revealed that multiple sequence types (STs), the most common of which was ST69 (n = 4) and ST10 (n = 2), followed by singletons belonging to ST372, ST101, ST569, ST218, and ST200. One isolate was assigned to a novel ST ST11351. A total of 66.7% isolates were positive for β-lactamase genes with 58.3% harboring the blaTEM1B gene and a single isolate the blaCTX−M−14 and blaCTX−M−55 extended-spectrum β-lactamase (ESBL) genes. One isolate was positive for the mcr-9 mobilized colistin resistance gene. Most antibiotic resistance genes (ARGs) were associated with mobile genetic support: class 1 integrons (In22, In54, In191, and In369), insertion sequences (ISs), and/or transposons (Tn402 or Tn21). A total of 31 virulence genes were identified across the study isolates, including those responsible for adhesion (lpfA, iha, and aggR), immunity (air, gad, and iss), and toxins (senB, vat, astA, and sat). The virulence genes were mostly associated with IS (IS1, IS3, IS91, IS66, IS630, and IS481) or prophages. Co-resistance to heavy metal/biocide, antibiotics were evident in several isolates. The phylogenomic analysis with South African E. coli isolates from different sources (animals, birds, and humans) revealed that isolates from this study mostly clustered with clinical isolates. Phylogenetics linked with metadata revealed that isolates did not cluster according to source but according to ST. The occurrence of pathogenic and MDR isolates in the WWTP effluent and the associated river is a public health concern.

Retrospective study of bacterial and fungal causes of abortion in domestic ruminants in northern regions of South Africa (2006-2016).

This initial retrospective study presents information on bacterial and fungal causes of abortion in domestic ruminants in South Africa over 10 years (2006-2016). A complete set of data was collected at the Faculty of Veterinary Science through a keyword search of pathology and bacteriology laboratory registers. Additional electronic data were received from an external laboratory. A total of 288 cases were recorded from six provinces. Overall diagnostic rate was 35.1%. In 14.6% of cases, histological evidence of an infectious process was found, but no aetiological agent was detected. Several cases did not include aetiological diagnoses because applicable diagnostic techniques were not available or not applied when necessary. Increased submission of placenta, as well as additional conventional and molecular diagnostic methods, can contribute to an improved diagnostic rate. In addition, the study highlights the superior significance of Brucella abortus as a major bovine pathogen in South Africa.

Predominance of Human Bocavirus Genotype 1 and 3 in Outpatient Children with Diarrhea from Rural Communities in South Africa, 2017-2018.

Human bocavirus (HBoV) is an emerging virus globally associated with diarrhea in young children. This study aims to investigate the prevalence of HBoV genotypes in children (≤5 years) from rural communities in South Africa (SA) suffering from acute gastroenteritis (AGE). A total of 141 fecal samples of children ≤5 years with acute gastroenteritis (AGE) were collected from rural primary health care facilities in the Vhembe district of SA between June 2017 and July 2018. Clinical symptoms and demographic data were also recorded. A total of 102 (72%) were outpatients, and 39 (28%) were hospitalized patients. Human bocavirus (HBoV) genotypes were determined using real-time multiplex PCR. DNA extracts of positive samples were confirmed by conventional PCR targeting the NS1 gene. Co-infection with other enteric viruses were determined in HBoV-positive samples using real-time PCR. HBoV was detected in eight (5.7%) children with AGE, of which three (37.5%) were HBoV1, three (37.5%) were HBoV3, and two (25%) were HBoV2. The majority of positive cases were identified in outpatients (62%) between the ages of 1 and 24 months. Co-infection in HBoV-positive samples with other enteric viruses included rotavirus (37.5%), adenovirus (37.5%), norovirus (25%), and astrovirus (12.5%). HBoV infections could be seen as a potential emerging diarrheal pathogen in South Africa. However, more studies are needed to understand the role of HBoV infections in children with AGE.

Population Biology and Genetic Variation of Spongospora subterranea f. sp. subterranea, the Causal Pathogen of Powdery Scab and Root Galls on Potatoes in South Africa.

Spongospora subterranea f. sp. subterranea, causal agent of powdery scab and root galls of potatoes, occurs worldwide and is responsible for quality and yield losses in potato production in South Africa. Despite being one of the most important potato pathogens in South Africa, little information is available on the genetic structure and diversity of S. subterranea f. sp. subterranea, which could provide insight into the factors shaping its evolution and the role of inoculum sources in disease development. A total of 172 samples were collected from four potato growing regions in South Africa. An additional 27 samples obtained from Colombia were included for comparative purposes. The samples were screened against six informative microsatellite (simple-sequence repeat) markers. Of the 172 samples obtained from potato growing regions in South Africa, there were 75 multilocus genotypes (MLGs), only 16 of which were shared between potato growing regions, indicating substantial gene flow and countrywide dispersal of the pathogen. The presence of common MLGs among the root- and tuber-derived samples indicated a lack of specialization of S. subterranea f. sp. subterranea to either tuber or root infection. Nei's unbiased estimates of gene diversity for the clone-corrected data were low and ranged from 0.24 to 0.38. Analysis of molecular variance and discriminant analysis of principal components showed no population differentiation between different potato growing regions in South Africa and between root- and tuber-derived genotypes. The presence of MLGs, high considerable genotypic diversity, and failure to reject the null hypothesis of random mating in most populations are indicative of some kind of recombination, either sexual or asexual, in these S. subterranea f. sp. subterranea populations. Information from this study provides new insights into the genetic structure and diversity of S. subterranea f. sp. subterranea in South Africa. Continuous monitoring of the pathogen population dynamics will be helpful in implementing effective region-specific management strategies for the pathogen, especially in the development of resistant potato cultivars.

Prevalence and risk factors contributing to antibiotic-resistant Staphylococcus aureus isolates from poultry meat products in South Africa, 2015-2016.

Staphylococcus aureus, including methicillin-resistant strains, has been detected in food products of animal origin globally. Limited data have been reported on the factors contributing to antibiotic resistance of food-borne pathogens in South Africa. The primary aim of this study was to determine the prevalence of S. aureus, including antibiotic-resistant strains, in poultry meat products as well as the evaluation of potential risk factors for contamination of poultry meat products with antibiotic-resistant S. aureus isolates. A cross-sectional investigation was conducted in municipalities located across the nine provinces of South Africa, which included abattoirs, meat processing facilities, retail outlets and cold stores at the major ports of entry into South Africa. Staphylococcus aureus isolates obtained from various poultry meat products were tested for susceptibility to 14 antibiotic compounds representing 10 antibiotic classes using the Kirby–Bauer disc diffusion method. Potential risk factors were evaluated using a logistic regression model. Of the 311 samples tested, 34.1% (n = 106) were positive for S. aureus (95% confidence interval [CI], 28.9% – 39.7%). Seventy-two of the 106 isolates were randomly selected for antibiotic sensitivity testing. Twenty-one per cent (n = 15) of the isolates selected for sensitivity testing were methicillin-resistant strains (95% CI, 12.2% – 32.0%). Multi-drug resistance was detected in 22.2% (n = 16) of these isolates tested (95% CI, 13.3% – 33.6%). Origin of the product (p = 0.160), type of meat product (p = 0.962), type of facility (p = 0.115) and facility hygiene practices (p = 0.484) were not significantly associated with contamination of poultry meat products with methicillin-resistant strains. The study provides baseline data for further studies on antibiotic resistance risk assessments for food-borne pathogens, including S. aureus, which should guide the implementation plans of the South African National Antimicrobial Resistance Strategy Framework, 2017–2024.

An overview of antimicrobial resistance surveillance among healthcare-associated pathogens in South Africa.

Healthcare-associated infections are a serious public health concern resulting in morbidity and mortality particularly in developing countries. The lack of information from Africa, the increasing rates of antimicrobial resistance and the emergence of new resistance mechanisms intensifies this concern warranting the need for vigorous standardised surveillance platforms that produce reliable and accurate data which can be used for addressing these concerns. The implementation of national treatment guidelines, policies, antimicrobial stewardship programmes and infection prevention and control practices within healthcare institutions require a platform from which it can draw information and direct its approach. In this review, the importance of standardised surveillance systems, the challenges faced in the application of a surveillance system and the condition (existence and nonexistence) of such systems in African countries is discussed. This review also reports on some South African data.

Diversity of Diatrypaceae Species Associated with Dieback of Grapevines in South Africa, with the Description of Eutypa cremea sp. nov.

Recent studies in grape-growing areas including Australia, California, and Spain have revealed an extensive diversity of Diatrypaceae species on grapevines showing dieback symptoms and cankers. However, in South Africa, little is known regarding the diversity of these species in vineyards. The aim of this study was, therefore, to identify and characterize Diatrypaceae species associated with dieback symptoms of grapevine in South Africa. Isolates were collected from dying spurs of grapevines aged 4 to 8 years old, grapevine wood showing wedge-shaped necrosis when cut in cross section as well as from perithecia on dead grapevine wood. The collected isolates were identified based on morphological characters and phylogenetic analyses of the internal transcribed spacer region (ITS) and β-tubulin gene. Seven Diatrypaceae species were identified on grapevine, namely Cryptovalsa ampelina, C. rabenhorstii, Eutypa consobrina, E. lata, E. cremea sp. nov., Eutypella citricola, and E. microtheca. The dying spurs yielded the highest diversity of species when compared with the wedge-shaped necrosis and/or perithecia. C. ampelina was the dominant species in the dying spurs, followed by E. citricola, whereas E. lata was the dominant species isolated from the wedge-shaped necroses and perithecia. These results confirm E. lata as an important grapevine canker pathogen in South Africa, but the frequent association of C. ampelina with spur dieback suggests that this pathogen plays a more prominent role in dieback than previously assumed. In some cases, more than one species were isolated from a single symptom, which suggests that interactions may be occurring leading to decline of grapevines. C. rabenhorstii, E. consobrina, E. citricola, E. microtheca, and E. cremea are reported for the first time on grapevine in South Africa.

Prevalence of antimicrobial resistance from bacterial culture and susceptibility records from horse samples in South Africa

The continuous increase in prevalence of antimicrobial resistant bacteria presents a significant public health problem and is an indicator that antimicrobial prudent usage guidelines are not being followed, especially in developing countries. Despite trends being available from numerous countries, there is little published for South Africa.This study was aimed at estimating the prevalence and trends of antimicrobial resistance from bacterial isolates from equine clinical samples submitted for culture and susceptibility testing to the veterinary bacteriology laboratory of the University of Pretoria. The study covered a period of seven years from 2007.A total of 1505 bacterial isolates were included in this study comprising isolates from 2007 (n=447); 2008 (n=285); 2009 (n=258); 2010 (n=102); 2011 (n=89); 2012 (n=248) and 2013 (n=76). For this study, multiple drug resistance was above 50% for all the isolates. The Cochran-Armitage test showed evidence of a significantly increasing trend in prevalence of resistance to several antimicrobial agents, including amikacin (E. coli, Staphylococcus), AMX/AMP (Corynebacteria, Lactobacillus and Salmonella), chloramphenicol (Enterococcus, E. coli, Pseudomonas, Streptococcus, Staphylococcus and Salmonella), enrofloxacin (E. coli, Staphylococcus, Salmonella and Pseudomonas) and gentamicin (Salmonella, Staphylococcus). The data obtained from this study is relevant to equine practitioners, as it helps enhance the body of veterinary knowledge pertaining to antimicrobial resistance in common equine pathogens in South Africa.

Investigation of Salmonella Enteritidis outbreaks in South Africa using multi-locus variable-number tandem-repeats analysis, 2013-2015

BackgroundSalmonella enterica serovar Enteritidis (Salmonella Enteritidis) has become a significant pathogen in South Africa, and the need for improved molecular surveillance of this pathogen has become important. Over the years, multi-locus variable-number tandem-repeats analysis (MLVA) has become a valuable molecular subtyping technique for Salmonella, particularly for highly homogenic serotypes such as Salmonella Enteritidis. This study describes the use of MLVA in the molecular epidemiological investigation of outbreak isolates in South Africa.MethodsBetween the years 2013 and 2015, the Centre for Enteric Diseases (CED) received 39 Salmonella Enteritidis isolates from seven foodborne illness outbreaks, which occurred in six provinces. MLVA was performed on all isolates.ResultsThree MLVA profiles (MLVA profiles 21, 22 and 28) were identified among the 39 isolates. MLVA profile 28 accounted for 77% (30/39) of the isolates. Isolates from a single outbreak were grouped into a single MLVA profile. A minimum spanning tree (MST) created from the MLVA data showed a close relationship between MLVA profiles 21, 22 and 28, with a single VNTR locus difference between them.ConclusionsMLVA has proven to be a reliable method for the molecular epidemiological investigation of Salmonella Enteritidis outbreaks in South Africa. These foodborne outbreaks emphasize the importance of the One Health approach as an essential component for combating the spread of zoonotic pathogens such as Salmonella Enteritidis.

The genetic landscape of Ceratocystis albifundus populations in South Africa reveals a recent fungal introduction event

Geographical range expansion or host shifts is amongst the various evolutionary forces that underlie numerous emerging diseases caused by fungal pathogens. In this regard, Ceratocystis albifundus, the causal agent of a serious wilt disease of Acacia mearnsii trees in Africa, was recently identified killing cultivated Protea cynaroides in the Western Cape (WC) Province of South Africa. Protea cynaroides is an important native plant in the area and a key component of the Cape Floristic Region. The appearance of this new disease outbreak, together with isolates of C. albifundus from natural ecosystems as well as plantations of nonnative trees, provided an opportunity to consider questions relating to the possible origin and movement of the pathogen in South Africa. Ten microsatellite markers were used to determine the genetic diversity, population structure, and possible gene flow in a collection of 193 C. albifundus isolates. All populations, other than those from the WC, showed high levels of genetic diversity. An intermediate level of gene flow was found amongst populations of the pathogen. The results suggest that a limited number of individuals have recently been introduced into the WC, resulting in a novel disease problem in the area.

Population genetic structure of Rhizoctonia solani AG 3-PT from potatoes in South Africa

Rhizoctonia solani AG 3-PT is an important potato pathogen causing significant yield and quality losses in potato production. However, little is known about the levels of genetic diversity and structure of this pathogen in South Africa. A total of 114 R. solani AG 3-PT isolates collected from four geographic regions were analysed for genetic diversity and structure using eight microsatellite loci. Microsatellite analysis found high intra-population genetic diversity, population differentiation and evidence of recombination. A total of 78 multilocus genotypes were identified with few shared among populations. Low levels of clonality (13–39 %) and high levels of population differentiation were observed among populations. Most of the loci were in Hardy–Weinberg equilibrium and all four populations showed evidence of a mixed reproductive mode of both clonality and recombination. The PCoA clustering method revealed genetically distinct geographic populations of R. solani AG 3-PT in South Africa. This study showed that populations of R. solani AG 3-PT in South Africa are genetically differentiated and disease management strategies should be applied accordingly. This is the first study of the population genetics of R. solani AG 3-PT in South Africa and results may help to develop knowledge-based disease management strategies.