Intratumor genetic heterogeneity and head and neck cancer relapse.

BACKGROUND: Head and neck squamous cell carcinomas are treated by surgery, radiotherapy (RT), chemoradiotherapy (CRT) or combinations thereof, but locoregional recurrences (LRs) occur in 30-40% of treated patients. We have previously shown that in approximately half of the LRs after CRT, cancer driver mutations are not shared with the index tumor. AIM: To investigate two possible explanations for these genetically unrelated relapses, treatment-induced genetic changes and intratumor genetic heterogeneity. METHODS: To investigate treatment-induced clonal DNA changes, we compared copy number alterations (CNAs) and mutations between primary and recurrent xenografted tumors after treatment with (C)RT. Intratumor genetic heterogeneity was studied by multi-region sequencing on DNA from 31 biopsies of 11 surgically treated tumors. RESULTS: Induction of clonal DNA changes by (C)RT was not observed in the xenograft models. Multi-region sequencing demonstrated variations in CNA profiles between paired biopsies of individual tumors, with copy number heterogeneity scores varying from 0.027 to 0.333. In total, 32 cancer driver mutations could be identified and were shared in all biopsies of each tumor. Remarkably, multi-clonal mutations in these same cancer driver genes were observed in 6 of 11 tumors. Genetically distinct heterogeneous cell cultures could also be established from single tumors, with different biomarker profiles and drug sensitivities. CONCLUSION: Intratumor genetic heterogeneity at the level of the cancer driver mutations might explain the discordant mutational profiles in LRs after CRT, while there are no indications in xenograft models that these changes are induced by CRT.

Utility of the BioFire® FilmArray® Pneumonia Panel plus assay for syndromic testing of lower respiratory tract infections in a low/middle-income setting.

Background: Determining lower respiratory tract infection (LRTI) aetiology is complex. Culture-based methods are laborious with poor sensitivity. Molecular assays improve detection of potential pathogens, but incorrect interpretation of results may lead to inappropriate antimicrobial therapy. Methods: The utility of the BioFire® FilmArray® Pneumonia Panel plus (FA-PP) to detect LRTI pathogens, and the potential impact on antimicrobial stewardship in a low-resource setting, were assessed. Routine LRT samples were included from adult patients with clinically suspected LRTI or with a concomitant blood culture at Groote Schuur Hospital and referring facilities. Culture and FA-PP results were compared, and pharmacy data analysed to determine appropriateness of antibiotic therapy. Results: There was an 80% correlation between cultured LRTI pathogens and the FA-PP bin ≥107 results. Compared with culture, the FA-PP detected substantially more pathogens (86.6% versus 17.9%) and produced a combined 100% positive percent agreement, and 88% negative percent agreement. The FA-PP detected bacterial/viral coinfections in 27% of samples. Correlation of FA-PP results with pharmacy data (n = 69) indicated a potential antibiotic change in 75% of cases, but this is difficult to accurately characterize without a 'gold standard' for treatment or complete clinical data. Conclusions: The FA-PP increased the number of positive samples with typical bacteria, but the semi-quantitative reporting algorithm does not describe the correlation between the different bin values and colonization versus infection. This complicates result interpretation and may lead to inappropriate antimicrobial treatment. This study highlights the potential positive impact of rapid molecular assays for routine care in lower-income settings, but also underscores the interpretive challenges associated with these tests.

Transplant Unit, Division of General Surgery, Department of Surgery, Faculty of Health Sciences, University of Cape Town, South Africa.

Organ and tissue donation depends on non-transplant clinicians to identify and timeously refer potential donors and to counsel families compassionately about the prognosis at end of life. Organ donation referral is often felt to be beyond the capacity of district-level hospital services. In this case series, we report on four referrals from a geographically remote, public sector district-level hospital, and review the identification, referral and consent process of potential donors after brain death, and also donors after circulatory death. For the one successfully consented donor we report on the donor work-up and management, and the outcome of the organ recovery and organ allocation process.

Improving primary care antimicrobial stewardship by implementing a peer audit and feedback intervention in Cape Town community healthcare centres.

BACKGROUND: The increasing prevalence of antibiotic resistance is a major threat to public health. Primary care, where 80% of antibiotics are consumed, is a pivotal setting to direct antimicrobial stewardship (AMS) efforts. However, the ideal model to improve antibiotic prescribing in primary care in low-resource settings is not known. OBJECTIVE: To implement a multidisciplinary audit and feedback AMS intervention with the aim to improve appropriate antibiotic prescribing at primary care level. METHODS: The intervention was implemented and monitored in 10 primary care centres of the Cape Town metropole between July 2017 and June 2019. The primary and secondary outcome measures were monthly adherence to a bundle of antibiotic quality process measures and monthly antibiotic consumption, respectively. Multidisciplinary audit and feedback meetings were initiated and integrated into facility clinical meetings. Two Excel tools were utilised to automatically calculate facility audit scores and consumption. Once a month, 10 antibiotic prescriptions were randomly selected for a peer review audit by the team. The prescriptions were audited for adherence to a bundle of seven antibiotic process measures using the standard treatment guidelines (STG) and Essential Medicines List (EML) as standard. Concurrently, primary care pharmacists monitored monthly antibiotic consumption by calculating defined daily doses (DDDs) per 100 prescriptions dispensed. Adherence and consumption feedback were regularly provided to the facilities. Learning collaboratives involving representative multidisciplinary teams were held twice-yearly. Pre-, baseline and post-intervention periods were defined as 6 months before, first 6 months and last 6 months of the study, respectively. RESULTS: The mean overall adherence increased from 19% (baseline) to 47% (post intervention) (p<0.001). Of the 2 077 prescriptions analysed, 33.7% had an antibiotic prescribed inappropriately. No diagnosis had been captured in patient notes, and the antibiotic chosen was not according to the STG and EML in 30.1% and 31.7% of cases, respectively. Seasonal variation was observed in prescribing adherence, with significantly lower adherence in winter and spring months (adjusted odds ratio 0.60). A reduction of 12.9 DDDs between the pre- and post-intervention periods (p=0.0084) was documented, which represented a 19.3% decrease in antibiotic consumption. CONCLUSION: The study demonstrated that peer reviewed audit and feedback is an effective AMS intervention to improve antibiotic prescribing in primary care in a low-resource setting. The intervention, utilising existing resources and involving multidisciplinary engagement, may be incorporated into existing quality improvement processes at facility level, to ensure sustainable change.

Using multi-event hydrologic and hydraulic signatures from water level sensors to diagnose locations of uncertainty in integrated urban drainage models used in living digital twins.

Digital twins of urban drainage systems require simulation models that can adequately replicate the physical system. All models have their limitations, and it is important to investigate when and where simulation results are acceptable and to communicate the level of performance transparently to end users. This paper first defines a classification of four possible 'locations of uncertainty' in integrated urban drainage models. It then develops a structured framework for identifying and diagnosing various types of errors. This framework compares model outputs with in-sewer water level observations based on hydrologic and hydraulic signatures. The approach is applied on a real case study in Odense, Denmark, with examples from three different system sites: a typical manhole, a small flushing chamber, and an internal overflow structure. This allows diagnosing different model errors ranging from issues in the underlying asset database and missing hydrologic processes to limitations in the model software implementation. Structured use of signatures is promising for continuous, iterative improvements of integrated urban drainage models. It also provides a transparent way to communicate the level of model adequacy to end users.

Hydatid brain cyst: A delayed diagnosis in a rural setting during COVID-19.

A previously healthy 10-year-old girl, living in a sheep-farming community in South Africa with exposure to dogs, presented to her local hospital with generalised tonic-clonic seizures. The initial clinical assessment and laboratory work-up were unremarkable. When she presented with further seizures 6 months later, attempts to arrange neuroimaging and specialist assessment were unsuccessful owing to restrictions on routine healthcare services during the SARS-CoV-2 nationwide lockdown. Subsequently, 11 months after her first presentation, she developed focal neurological signs suggestive of raised intracranial pressure. A brain computed tomography scan revealed a left-sided cerebral cyst and imminent tonsillar herniation. An emergency burr-hole procedure was performed to relieve the raised intracranial pressure, followed by definitive neurosurgical excision of cysts. Hydatid protoscolices and hooklets were seen on microscopy of cyst fluid, and treatment with albendazole and praziquantel was initiated. While her infection was treated successfully, long-term sequelae including permanent blindness and hemiparesis could potentially have been prevented with early neuroimaging and surgical intervention.

Statement on analysis and interpretation of clinical human gastrointestinal microbiome testing using next-generation sequencing in South Africa.

Advances in DNA sequencing technologies and computational tools over the past few years have led to vast improvements in the metagenomic analysis of the human microbiota. While this has also significantly improved our understanding of the role of the host-microbiome interaction in health and disease, the current clinical expectation is that testing, particularly of the gastrointestinal biome, can be used to diagnose, manage and treat patients. The authors outline the available technologies and highlight current limitations of these techniques to address this clinical demand. Through understanding the limitations of and need for more research and data collection, one can improve the appropriate utilisation and interpretation, as well as the current rational clinical application of these techniques.

The Association between Tumour Markers and Meta-iodobenzylguanidine Scans in South African Children with High-risk Neuroblastoma.

AIMS: Diagnostic and post-induction 123I-meta-iodobenzylguanidine (123I-mIBG) scans have prognostic significance in the treatment of neuroblastoma, but data from low- and middle-income countries are limited due to resource constraints. The aim of this study was to determine the association between neuroblastoma-associated tumour markers (lactate dehydrogenase [LDH], ferritin and MYCN amplification) and 123I-mIBG scans (modified Curie scores and metastatic disease patterns) in predicting complete metastatic response rates (mCR) and overall survival. MATERIALS AND METHODS: Two hundred and ninety patients diagnosed with high-risk neuroblastoma in South Africa between January 2000 and May 2018 and a subanalysis of 78 patients with diagnostic 123I-mIBG scans were included. Data collection included LDH, ferritin and MYCN amplification at diagnosis. Two nuclear physicians independently determined the modified Curie scores and pattern of distribution for each diagnostic and post-induction 123I-mIBG scans with high inter-rater agreement (r = 0.952) and reliability (K = 0.805). The cut-off values for the diagnostic and post-induction modified Curie scores of ≥7.0 (P = 0.026) and 3 (P = 0.009), respectively, were generated. The association between the tumour markers and the modified Curie score of the 123I-mIBG scans was determined using post-induction mCR and 2-year overall survival. RESULTS: Diagnostic LDH (P < 0.001), ferritin (P < 0.001) and the diagnostic modified Curie scores (P = 0.019) significantly predicted mCR. Only ferritin correlated with diagnostic modified Curie scores (P = 0.003) but had a low correlation coefficient of 0.353. On multivariable analysis, the only significant covariate for 2-year overall survival at diagnosis was LDH <750 U/l (P = 0.024). A post-induction chemotherapy modified Curie score ≤3.0 had a 2-year overall survival of 46.2% compared with 30.8% for a score >3.0 (P = 0.484). CONCLUSION: LDH, ferritin and the diagnostic 123I-mIBG scans significantly predicted mCR, but only LDH predicted 2-year overall survival. Ferritin and the modified Curie scores correlated with each other. MYCN amplification neither correlated with any aspect of the 123I-mIBG scans nor significantly predicted mCR or 2-year overall survival. LDH and ferritin are therefore appropriate neuroblastoma tumour markers to be used in low- and middle-income countries with limited or no access to mIBG scans and/or MYCN amplification studies.

Using ceftazidime-avibactam for persistent carbapenem-resistant Serratia marcescens infection highlights antimicrobial stewardship challenges with new beta-lactam-inhibitor combination antibiotics.

The newer beta-lactam-inhibitor combination (BLIC) antibiotics are available in South Africa (SA) for the treatment of carbapenem-resistant Enterobacterales infections. We describe the successful use of ceftazidime-avibactam (CA) for the treatment of a child with persistent carbapenem-resistant Serratia marcescens bacteraemia, and the challenges faced using this lifesaving antibiotic, including access to susceptibility testing, procurement process, cost and complexity of deciding when, how and for how long to use it. Furthermore, the burden of carbapenem resistance is increasing in SA, and inappropriate use of CA and other newer BLIC antibiotics, such as ceftolozane-tazobactam, will inevitably endanger their longevity. A careful balance must be struck between removing unnecessary obstacles and delays in initiating these antibiotics for life-threatening infections, and additional antimicrobial stewardship-guided interventions aimed at preserving their therapeutic use.

Prediction admission in the older population in the Emergency Department: the CLEARED tool.

BACKGROUND: Length of stay (LOS) in the Emergency Department (ED) is correlated with an extended in-hospital LOS and may even increase 30-day mortality. Older patients represent a growing population in the ED and they are especially at risk of adverse outcomes. Screening tools that adequately predict admission could help reduce waiting times in the ED and reduce time to treatment. We aimed to develop and validate a clinical prediction tool for admission, applicable to the aged patient population in the ED. METHODS: Data from 7,606 ED visits of patients aged 70 years and older between 2012 and 2014 were used to develop the CLEARED tool. Model performance was assessed with discrimination using logistic regression and calibration. The model was internally validated by bootstrap resampling in Erasmus Medical Center and externally validated at two other hospitals, Medisch Spectrum Twente (MST) and Leiden University Medical Centre (LUMC). RESULTS: CLEARED contains 10 predictors: body temperature, heart rate, diastolic blood pressure, systolic blood pressure, oxygen saturation, respiratory rate, referral status, the Manchester Triage System category, and the need for laboratory or radiology testing. The internally validated area under the curve (AUC) was 0.766 (95% CI [0.759;0.781]). External validation in MST showed an AUC of 0.797 and in LUMC, an AUC of 0.725. CONCLUSIONS: The developed CLEARED tool reliably predicts admission in elderly patients visiting the ED. It is a promising prompt, although further research is needed to implement the tool and to investigate the benefits in terms of reduction of crowding and LOS in the ED.

The ethicolegal framework relevant to human faecal microbiota transplants in South Africa: Part 3. Stool as a 'drug' or medicine.

The purpose of this article, the last in a series of three exploring the legal framework for the regulation of faecal microbiota transplantation (FMT) in South Africa (SA), is to determine the regulatory framework that applies to microbial-based treatments involving a level of manipulation that exceeds that of basic stool transplantation, e.g. processed FMT-derived products in capsule form. The article highlights the legal requirements for the registration of these products as biological medicines in SA law. Although human stool banks are not regulated in terms of the National Health Act 61 of 2003 (NHA) and regulations, the earlier articles point out that human stool fits the definition of human tissue and human biological material as defined by the NHA. For this reason, stool banks should be considered tissue banks in terms of the NHA and regulations. Healthcare practitioners and researchers involved in FMT banking and transplantation should strive to comply with these regulations in the absence of clear legal direction at present.

The ethicolegal framework relevant to human faecal microbiota transplants in South Africa: Part 2. Human stool as tissue?

Faecal microbiota transplantation (FMT) has been shown to be an effective treatment for recurrent Clostridioides difficile infection. The purpose of this article, the second of a series of three articles, is to explore the legal framework governing human FMT in South Africa (SA). FMT involves different modes of administration that require different regulatory considerations. The focus of this article is to explore the legal classification of human stool as tissue in terms of the National Health Act 61 of 2003, as well as the regulation of human stool banks as tissue banks. The article concludes with specific recommendations aimed at improving the current regulatory vacuum relating to the regulation of FMT in SA.

The ethicolegal framework relevant to human faecal microbiota transplants in South Africa: Part 1. A legal vacuum.

The legal regulation of faecal microbiota transplantation (FMT) in South Africa (SA) is currently unclear. The purpose of this article, the first of three in a series, is to explore the nature, role and clinical application of FMT in SA in order to determine, from a legal perspective, the appropriate regulatory pathways governing FMT as a procedure that may combine approaches for the treatment of drugs, human tissue for transplantation, or clinical treatment as part of the practice of medicine. FMT has been shown to be a novel, safe and effective treatment for recurrent Clostridioides difficile infection (CDI). Stool banks are instrumental in enabling access to FMT for patients and clinicians and help to catalyse research in the microbiome. However, the regulatory landscape in SA remains unclear. Microbial therapies such as FMT are necessary, especially in a time of rising microbiome-associated inflammatory diseases and increasing resistance to traditional antibiotics. FMT is now considered as part of the standard of care for recurrent CDI overseas, but is currently only being used for research purposes in a minority of clinical cases of CDI in SA. This article, which lays the foundation for consideration of this question in three parts, suggests that the relevant regulatory system would depend on the categorisation of human stool as tissue, the exact composition of the FMT, how it is administered to patients, and the relevant levels of manipulation of the stool for FMT-derived products.

Implementing a multi-faceted framework for proprietorship of hand hygiene compliance in a network of South African hospitals: leveraging the Ubuntu philosophy.

BACKGROUND: Given the lack of hospital-wide ownership and shortage of nurses, the ideal model for large-scale implementation of hand hygiene (HH) behaviour change in low- and middle-income countries is unknown. AIM: The aim of the multi-modal strategy was to engender hospital accountability for HH compliance. METHODS: The quasi-experimental study was conducted in 50 South African hospitals (November 2015 to July 2017) and involved five overlapping phases: executive governance and corporate behaviour change; group-wide systematic situational analysis; development of an electronic-assisted direct-observed data collection and analysis application; launch and implementation; and accountable governance. Measurement of intra- and inter-hospital variance to six HH opportunities was calculated and data compliance dashboards were e-mailed weekly to hospital leadership teams to provide feedback of recorded HH compliance and behaviour to frontline teams. Baseline comparison (July 2016) of compliance was compared versus post-implementation (July 2017). FINDINGS: Baseline HH compliance of ≤60% was documented for 16% (8/50) of hospitals, whereas overall, 48% (24/50) of hospitals demonstrated a significant improvement (P < 0.01). Over the 13-month observation period, 523,422 observations were recorded with a mean rate of 277 ± 223 observations per 1000 patient-days. The group mean composite compliance improved by 7.8% (P < 0.01) from 77.4% ± 12.8 to 85.2% ± 8.8 between July 2016 and July 2017, respectively. CONCLUSION: Implementation of a multi-faceted HH model in a large, diverse group of South African hospitals translated into changes in the organizational systems and accountability, standardized HH compliance management and feedback that led to HH proprietorship.

Prediction models for mortality in adult patients visiting the Emergency Department: a systematic review.

We provide a systematic overview of literature on prediction models for mortality in the Emergency Department (ED). We searched various databases for observational studies in the ED or similar setting describing prediction models for short-term mortality (up to 30 days or in-hospital mortality) in a non-trauma population. We used the CHARMS-checklist for quality assessment. We found a total of 14.768 articles and included 17 articles, describing 22 models. Model performance ranged from AUC 0.63-0.93. Most articles had a moderate risk of bias in one or more domains. The full model and PARIS model performed best, but are not yet ready for implementation. There is a need for validation studies to compare multiple prediction models and to evaluate their accuracy.

Rational use of the fluoroquinolones.

The systemic fluoroquinolones (FQs) have recently been reported to be associated with significant side-effects in susceptible individuals. This has prompted the Food and Drug Administration (FDA) in the USA and the European Medicines Agency (EMA) to issue warnings regarding their use. The FQs should not be used for common bacterial infections, such as urinary tract infections, travellers' diarrhoea and upper and lower respiratory tract infections, unless it is not possible to use another oral agent. There are situations, however, in which these agents are not only effective, but their benefit outweighs the risk. These include the management of conditions such as acute prostatitis, typhoid fever, prosthetic joint infections, multidrug-resistant tuberculosis, certain hospital-acquired infections and situations where the organism is susceptible to FQs, which could then be administered orally. Alternatively, the patient would have to be admitted to hospital for parenteral therapy.

No direction specific costs in trans-saccadic memory.

Even though we frequently execute saccades, we perceive the external world as coherent and stable. An important mechanism of trans-saccadic perception is spatial remapping: the process of updating information across eye movements. Previous studies have indicated a right hemispheric dominance for spatial remapping, which has been proposed to translate into enhanced trans-saccadic memory for locations that are remapped into the right compared to the left hemisphere in healthy participants. Previous study designs suffered from several limitations, however (i.e. multiple eye movements had to be made instead of one, fixations were not controlled for, and ceiling effects were likely present). We therefore compared accuracy of trans-saccadic memory for central items after left- versus rightward eye movements, and secondary, for items that were remapped within the left versus right visual field. Participants memorized the location of a briefly presented item, made one saccade, and subsequently decided in what direction the item had shifted. We used a staircase to adjust task difficulty. Bayesian repeated measures ANOVAs were used to compare between left versus right eye movements and items in the left versus right visual field. We found most evidence against directional differences in trans-saccadic memory (BF10 = 0.23). We found some evidence suggestive of enhanced trans-saccadic memory for items that were remapped within the left compared to the right visual field (BF10 = 4.00). The latter result could be explained by a leftward spatial attention bias. As such, the hypothesized right hemispheric dominance for spatial remapping does not result in asymmetric trans-saccadic memory capacities in healthy participants.

[Treatment of post-traumatic stress disorder in people with intellectual disability]. / Behandeling van posttraumatische stressstoornis bij mensen met een laag IQ.

BACKGROUND: Patients with borderline intellectual functioning (BIF) or intellectual disability (ID) are more likely to develop post-traumatic stress disorder (PTSD). However, co-occurrence of BIF/ID and PTSD symptoms often leads to exclusion for treatment in regular mental health care centers.
AIM: To determine whether standard treatment programs for PTSD can be used in the treatment of patients with BIF/ID.
METHOD: Qualitative review of good practices, scientific literature and recent reports about BIF, ID and PTSD.
RESULTS: Literature on evidence-based treatment programs for PTSD suggests that there is no need to be reluctant in starting treatment in patients with BIF/ID. Adjustment of communication and tempo is recommended.
CONCLUSION: There is reason to believe that standard treatment can be used in treating patients with a low IQ. More research to confirm this assumption is necessary, taken into account the size of this patient group.