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Background: Picture archiving and communication systems (PACS) are now an established means of capturing, storing, distribution and viewing of all radiology images. The study was conducted in a quaternary hospital, Charlotte Maxeke Johannesburg Academic Hospital (CMJAH), part of the University of the Witwatersrand teaching circuit, in South Africa. Objectives: To measure the clinicians’ perceived benefits and challenges of PACS. To document perceived views on how the current PACS can be improved. Method: This was a cross-sectional observational study over a period of 5 months from September 2021 to January 2022 carried out at CMJAH. Questionnaires were distributed to referring clinicians with PACS experience. Descriptive statistics was conducted. Categorical variables were presented as frequency and percentages. The continuous variables were presented as means ± standard deviation. Results: A survey with a response rate of 54% found the benefits most reported by clinicians were improved patient care, less time needed to review an exam, improved image comparison and consultation efficiency. With respect to perceived challenges, the unavailability of images at the bedside, problems with access and the lack of advanced image manipulating software were noted. The most frequent recommendations on improvements focused on the aforementioned challenges. Conclusion: Hospital-wide PACS was viewed beneficial by most clinicians. Nonetheless, there are a few aspects that deserve attention to improve the functionality and access of the system. Contribution: The findings will assist in future hospital or provincial-wide PACS deployment projects.

Background: Stereotactic breast biopsies have become the gold standard for tissue diagnosis in non-palpable, sonographically occult breast abnormalities seen on mammogram. Only limited data exist in South Africa on the correlation between imaging findings and stereotactic biopsy histology. Objectives: To describe the mammographic findings and histological diagnosis in patients who underwent stereotactic breast biopsy at a referral hospital. In addition, to evaluate the proportion of malignancy in each Breast Imaging Reporting and Data System (BI-RADS) category. Method: A retrospective review of stereotactic breast biopsies was performed. Imaging characteristics (including BI-RADS category) and histological diagnosis were recorded. Using histopathology, cases were classified as benign, high-risk or malignant. Results: A total of 131 biopsies, from 123 patients, were included in the study. Most biopsies were performed on asymptomatic patients (79.3%, 104/131). The majority were categorised as BI-RADS 4 and demonstrated calcifications. Histology revealed a malignant diagnosis in 40 (30.5%) patients, a high-risk lesion in 8 (6.1%) patients and a benign diagnosis in 83 (63.4%) patients. There was a stepwise increase in the proportion of malignancy from BI-RADS category 3 to 5. When compared with surgical histology, the stereotactic biopsies demonstrated an overall ductal carcinoma in situ (DCIS) underestimation rate of 10.3%. Conclusion: Despite resource restrictions, stereotactic breast biopsies performed in a South African context produce radiological-pathological concordance in keeping with BI-RADS guidelines, as well as with local and international studies.

Background: Globally, adults presenting with seizures account for 1% – 2% of visits to emergency departments (EDs), of which 25% are new-onset seizures. Neuroimaging is essential as part of the initial workup. Multiple studies have demonstrated abnormal CT brain (CTB) findings in these patients. Objectives: To review the CTB findings in adults presenting with new-onset seizures in a resource restricted setting. Method: A retrospective review of 531 CTBs was conducted at a tertiary hospital in Gauteng on adults presenting to the ED with new-onset seizures. Results: The mean age of the patients was 45.6 ± 17.1 years, and the male to female ratio was 1.2:1. Generalised and focal seizure types were almost equally represented. Of the total 531 patients, 168 (31.6%) were HIV positive. The CTB findings were abnormal in 257 (48.4%) patients, albeit vascular pathology accounted for 21.9%. Infective pathology accounted for 14.1% with a statistically significant association with HIV (p = 0.003). Trauma related pathology was 2.4%, whilst neoplastic pathology was seen in 3.0%. Other causes included congenital pathology, calcifications, atrophy and gliosis. Clinical factors associated with abnormal CTB findings were age ≥ 40 years, HIV infection, hypertension, focal seizures, low Glasgow Coma Scale (GCS), raised cerebrospinal fluid (CSF) protein and presence of lymphocytes. Conclusion: A high yield of abnormal CTB findings was noted in adult patients who presented with new-onset seizures, supporting the use of urgent CTB in patients with certain clinical risk factors. Patients without these risk factors can be scanned within 24–48 h in a resource restricted setting.

Background: South Africa bares a significant burden of HIV and imaging is commonly performed as part of the workup for respiratory distress. Objectives: The aim of this study was to document the prevalence of pulmonary thrombo-embolic disease (PTED) and other findings in HIV-infected patients referred for CT pulmonary angiography (CTPA) for suspected PTED. Method: Forty CTPA studies of documented HIV-infected individuals investigated for suspected PTED during a 1-year period were retrieved, anonymised and interpreted by three consultant radiologists. Inter-reader reliability was calculated using Free Marginal multi-rater Kappa. Results: Fourteen of the forty cases (35%) were positive for PTED. In the pulmonary embolism (PE)-positive group, 57.14% had peripheral disease and 42.86% had both peripheral and central disease. Associated findings in the PE-positive cases were pulmonary infarcts (17.5%), mosaic attenuation (17.5%) and linear atelectasis (7.5%). The most common incidental findings were solid pulmonary nodules (52.5%), non-wedge-shaped consolidation (45%), cardiomegaly (52.5%) and enlarged intra-thoracic lymph nodes (52.5%). Thirty per cent of the study population had findings related directly to the presence of PTED, whilst most cases in the study (77.5%) had pulmonary findings unrelated to PTED. In the PE-negative cases, 55% reported emergent findings that warranted immediate or urgent medical attention. Conclusion: Computed tomography pulmonary angiography imaging is critical for diagnosing PE. However, further investigation into the judicious application of CTPA in HIV-infected patients with suspected PTED is required, as CTPA findings in most of the cases in this study were unrelated to PE.

Purpose: Breast cancer is the leading cause of cancer death in women worldwide, with high mortality in low- and middle-income countries because of a lack of detection, diagnosis, and treatment. With mammography unavailable, ultrasound offers an alternative for downstaging. The literature reports successful training in various domains, but a focus on the breast is novel. We assessed the feasibility (knowledge acquisition, perceived usefulness, and self-efficacy) of breast ultrasound training for nonphysician providers. Methods: Training was implemented for 12 providers at Hlokomela Clinic in Hoedspruit, South Africa, over 3 weeks. Didactic presentations and example cases were followed by a presurvey and test (n = 12). All providers received hands-on training with nurses as models; five providers trained with patients. A post-test (n = 12) assessed knowledge acquisition and a postsurvey (n = 10) assessed perceived program usefulness and provider self-efficacy. Results: The pre- to post-test averages improved by 68% in total and in four competencies (foundational knowledge, descriptive categories, benign v malignant, and lesion identification). On the postsurvey, providers expressed that ultrasound could significantly influence breast cancer detection (9.1 out of 10), treatment (7.9 out of 10), and survival (8.7 out of 10) in their community and endorsed moderate confidence in their scanning (6.3 out of 10) and interpreting abilities (5.6 out of 10). Conclusion: Our research supports the feasibility of breast ultrasound training as part of a breast education program in low- and middle-income countries. Pre- and post-test results and observed proficiency indicate that training nonphysician providers is achievable; postsurvey responses indicate program acceptance, community-based ownership, and provider self-efficacy with ultrasound. Future work may show that breast ultrasound is viable for early detection where mammography is unavailable.

Background: Stroke presents commonly to the emergency department (ED), and is a common cause of morbidity and mortality in South Africa. Early ED presentation and early neuroimaging are required in order for thrombolysis to be a potential therapeutic modality. Objectives: To determine the time to ED presentation, time to computed tomography (CT) scan and the potential influencing factors for patients with stroke. Methods: A retrospective record review of all patients who presented with clinical features of stroke to a tertiary academic ED in Johannesburg, South Africa, from 01 January to 31 December 2014. Results: Data from 232 eligible stroke patients were analysed. The median time to presentation to the ED was 33 h with the majority of patients (81.3%) presenting after the 4.5 h window for thrombolysis. The median time to CT was 8 h. Only 3.9% of patients had a CT scan within one hour of arrival. Patients with loss of consciousness were associated with earlier hospital presentation (p = 0.001). None of the patients were thrombolysed. Conclusion: Patients with stroke commonly present late to hospital. If we are to make a difference in this group of vulnerable patients, further education and training needs to be emphasised regarding ‘time is brain’. Communication and commitment is also required by the emergency medical services, ED and radiology staff in order to prioritise stroke patients and to reduce delays.

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The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.

BackgroundCupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source.Methodology/principal findingsIts genome consists of four replicons (two chromosomes and two plasmids) containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common to the four genomes compared (C. necator JMP134, C. necator H16, C. metallidurans CH34, R. solanacearum GMI1000). Although secondary chromosomes found in the Cupriavidus, Ralstonia, and Burkholderia lineages are all derived from plasmids, analyses of the plasmid partition proteins located on those chromosomes indicate that different plasmids gave rise to the secondary chromosomes in each lineage. The C. necator JMP134 genome contains 300 genes putatively involved in the catabolism of aromatic compounds and encodes most of the central ring-cleavage pathways. This strain also shows additional metabolic capabilities towards alicyclic compounds and the potential for catabolism of almost all proteinogenic amino acids. This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment. From the comparison of Cupriavidus genomes, it is possible to state that a broad metabolic capability is a general trait for Cupriavidus genus, however certain specialization towards a nutritional niche (xenobiotics degradation, chemolithoautotrophy or symbiotic nitrogen fixation) seems to be shaped mostly by the acquisition of "specialized" plasmids.Conclusions/significanceThe availability of the complete genome sequence for C. necator JMP134 provides the groundwork for further elucidation of the mechanisms and regulation of chloroaromatic compound biodegradation.

Methanohalophilus mahii is the type species of the genus Methanohalophilus, which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLPT was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.

BACKGROUND:Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens. METHODOLOGY/PRINCIPAL FINDINGS:In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales. CONCLUSIONS/SIGNIFICANCE:Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).

Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.

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