A challenging case of hypercalcaemia

Hypercalcaemia is not uncommon in clinical practice. The majority of cases are accounted for by hyperparathyroidism and malignancy. The patient discussed below presented with an unusual case of hypercalcaemia.http://www.journals.co.za/ej/ejour_m_jemdsa.htmlam201

An unexpected acute coronary syndrome

Acute coronary syndromes due to coronary artery vasospasm occur rarely and are difficult to diagnose in the acute setting. We present a patient with hypocalcaemia-induced coronary artery vasospasm, which resulted in an acute ST-elevation myocardial infarction. This was reversible upon administering intravenous calcium, with no long-term cardiac consequences for our patient.http://www.sajcc.org.zaam2020Internal Medicin

The association between elevated troponin levels and all cause 30 day mortality in critically ill patients seen at an Academic Hospital – a prospective cohort study

PURPOSES : Elevated cardiac troponins have been shown to be associated with mortality in critical care, but its utility is not well established, especially in the setting of renal failure. This study aimed to examine the relationship between an early elevated troponin level and all cause 30 day mortality in critically ill patients, and in the subgroup of patients with renal failure. METHODS : Serum troponin levels were collected from all patients referred to a critical care team, be they medical or surgical, within 48 hours of referral. The study was a prospective cohort over a six month period. Patients’ outcome was followed up to 30 days post enrolment. RESULTS : A total of 202 patients were enrolled in the study over a period of 6 months. One hundred and thirty one patients survived to 30 days (64.9%). A statistically significant association with troponin elevation and mortality was found (p = 0.008). Higher levels of troponin were also associated with higher mortality in the subjects studied. Once adjusted for renal failure, a relative risk of death of 2.27 (p = 0.012) was found with troponin values above 325 ng/L.http://www.oatext.com/Pulmonary-and-Critical-Care-Medicine-PCCM.phpam2018Internal Medicin

Acute intermittent porphyria mimicking Guillain–Barré syndrome in a HIV patient

The diagnosis of porphyria remains challenging as the condition is characterized by a myriad of clinical and biochemical features. More importantly, an acute attack is associated with increased morbidity and mortality. Misdiagnosis of porphyria poses an ongoing problem. We describe a 42-year-old Black female South African patient who presented to Steve Biko Academic Hospital in Pretoria, on the 16 July 2014 with a clinical problem of acute paraparesis. On admission, she had absent reflexes, bilateral cranial nerve VII fallout, patchy sensory fallout and faecal incontinence. When her magnetic resonance imaging of the brain and cervical spine showed no signs suggestive of acute disseminated encephalomyelitis, a diagnosis of Guillain–Barré syndrome was made. On the 21 July her condition deteriorated to the point where she needed ventilator support. She also developed a pulmonary embolism and was treated. Due to deterioration of her condition, urine was sent for porphobilinogen test. This was clearly positive. The diagnosis of acute intermittent porphyria was eventually made. This case highlights the complexity related to the diagnosis of porphyria. It confirms that the diagnosis is often incidental and in a vast majority of patients, neurological complications preceded the final biochemical diagnosis.http://www.elsevier.com/locate/hivarPhysiologyInternal MedicineNeurolog

Characteristics and outcomes of patients admitted to a tertiary academic hospital in Pretoria with HIV and severe pneumonia : a retrospective cohort study

BACKGROUND : Human immunodeficiency virus (HIV) contributes significantly to morbidity and mortality in South Africa. Pneumonia and opportunistic infections remain a major cause for hospital admission among those living with HIV, even in the era of the widespread availability of antiretroviral therapy. METHODS : In this retrospective cohort study, the records of patients admitted with HIV and severe pneumonia, requiring high care/intensive care admission, during a period of 12 months (February 2018 to January 2019) were reviewed. Demographic details, antiretroviral use, HIV viral load, CD4 count, sputum culture results and radiological imaging of patients were recorded. Data was analysed to determine variables associated with mortality. RESULTS : One hundred and seventeen patient records were reviewed for this study. The patients were young (mean age 38.3 years), had advanced disease with low CD4 counts (mean 120.2 cells/mm3) and high HIV viral loads (mean 594,973.7 copies/mL). Only 36.9% (42/117) were on highly active antiretroviral therapy (HAART) on presentation to the hospital. Mycobacterium tuberculosis (M. tuberculosis) was found to be the cause for pneumonia in 35% (41/117), whilst Pneumocystis jirovecii (P. jirovecii) was found in 21.4% (25/117). Bacterial pneumonia was the cause in 17.1% (20/117) of patients while no specific aetiology was found in 26.6% (31/117) of patients in the cohort. Mortality among the cohort studied was high (40.1%) and the average length of stay in hospital in excess of two weeks. The need for ICU admission, ventilation and CMV viremia was associated with increased mortality. Chest X-ray findings did not correlate with the aetiology of pneumonia, but multiple B-lines on lung ultrasound correlated with P. jirovecii as an aetiology and there was a signal that pleural effusion with fibrin stranding predicts tuberculosis. CONCLUSIONS : Patients studied presented with advanced HIV and were often naïve to antiretroviral therapy. Mortality in this cohort of young patients was high, which emphasis the need for earlier diagnosis and treatment of HIV at a primary care level. Lung ultrasound may have clinical utility in the management of patients with HIV and pneumonia, particularly to diagnose P. jirovecii as an aetiology.http://www.biomedcentral.com/bmcinfectdisam2023Internal MedicineMedical Microbiolog

Surveillance of catheter-related infections : the supplementary role of the microbiology laboratory

BACKGROUND : The burden of catheter-related infections (CRIs) in developing countries is severe. In South Africa, a standardised surveillance definition does not exist and the collection of catheter days is challenging. The aim of the study was to provide baseline data on the prevalence of CRIs and to describe the epidemiology of CRI events within a tertiary academic hospital. METHODS : Surveillance was laboratory-based and conducted for a six month period. A microbiologically confirmed CRBSI (MC-CRBSI) event was defined as the isolation of the same microorganism from the catheter and concomitant blood cultures (BCs), within 48 h of catheter removal, which were not related to an infection at another site. RESULTS : A total of 508 catheters, removed from 332 patients, were processed by the laboratory, of which only 50% (253/508 removed from 143/332 patients) of the catheters were accompanied by BCs within 48 h. Sixty-five episodes of MC-CRBSI in 57 patients were detected, involving 71 catheters and 195 microbial isolates. The institutional prevalence rate was 3.7 episodes per 1 000 admissions and 5.8 episodes per 10 000 in-patient days. Catheter day data was collected in only six wards of the hospital. The pooled laboratory incidence was 10.1 MC-CRBSI episodes per 1 000 catheter days, whereas the hospital-based central line-associated bloodstream infection (CLABSI) rate was pooled at 5.7 episodes per 1 000 catheter days. The majority of patients had an underlying gastro-intestinal condition (33%; 19/56) with a non-tunnelled, triple-lumen central venous catheter, placed in the subclavian vein (38%; 27/71). The most predominant pathogen was methicillin-resistant Staphylococcus epidermidis (28%; 55/195), followed by extensively-drug resistant Acinetobacter baumannii (18%; 35/195). CONCLUSIONS : Catheter-related infection prevention and control efforts require urgent attention, not only to keep patients safe from preventable harm, but to prevent the spread of multidrug resistant microorganisms.RESCOM,Faculty of Health Science, UP, National Health Laboratory Service (NHLS) and the National Research Foundation (NRF).http://www.biomedcentral.com/bmcinfectdis/hb201

The lung microbiome in HIV‑positive patients with active pulmonary tuberculosis

Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection. Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN, Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for 16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared to the HIV-positive control cohort. Microbial community structure was also distinct from the control cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter, Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIVpositive control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the HIV-positive control cohort without PTB, with an associated loss of microbial diversity.DATA AVAILABILITY : The datasets generated and analysed during the current study are available in the University of Pretoria data repository and can be accessed at https://doi.org/10.25403/UPresearchdata.19491317.v1.The Infectious diseases Research Fund.http://www.nature.com/scientificreportsam2023BiochemistryGeneticsInternal MedicineMedical MicrobiologyMicrobiology and Plant Patholog

Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome

BACKGROUND : Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients. METHODS : Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method. RESULTS : Statistically significant differences were observed in alpha diversity when targeted metagenomics and ISPro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the ISPro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly. CONCLUSIONS : It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.SUPPLEMENTARY MATERIAL: Table S1. Inclusion and exclusion criteria for COPD patients in this study. Table S2. Clinical characteristic of patients. Table S3. Comparison of the number of amplicons and operational taxonomic units for each sample for the targeted metagenomics and IS-Pro methods. Figure S1. Relative abundance of specific phyla in the sputum microbiome of COPD participants as detected by targeted metagenomics and IS-Pro methods (n = 23). The dots represent the different abundances of each sample, according to the different phyla. Phyla that are depicted with a single line on the y-axis were not present in any samples for that method. Figure S2. Bar plots showing the relative abundance of genera in the sputum microbiome of COPD participants as characterised by targeted metagenomics and IS-Pro methods (n = 23). The operational taxonomic units that could not be classified at a genus level are indicated as NA on the graph. Figure S3. The distribution of the unclassified operational taxonomic units (OTUs) at a class level of the sputum microbiome of COPD participants for targeted metagenomics and IS-Pro methods by phyla. At a class level, all the OTUs from targeted metagenomics could be classified.National Health Laboratory Service of South Africa (NHLS) Research Trusthttps://bmcmicrobiol.biomedcentral.comam2022Internal MedicineMedical Microbiolog

Severe porphyric neuropathy - importance of screening for porphyria in Guillain-Barré syndrome

The hepatic porphyrias are a group of rare metabolic disorders, each of which is associated with a specific enzymatic alteration in the haem biosynthesis pathway. In South Africa (SA), a high incidence of variegate porphyria (VP) is seen as a result of a founder effect, but acute intermittent porphyria (AIP) is also encountered. The development of acute neurovisceral attacks is related to environmental factors, including medications, hormones and diet. A possible manifestation of a severe attack is rapidly progressing quadriparesis, which may mimic Guillain-Barré syndrome. We present four such cases, highlighting that acute porphyria should be considered in the differential diagnosis of Guillain-Barré syndrome. Three patients presented to Steve Biko Academic Hospital, Pretoria, SA, with progressive quadriparesis, and one to a private hospital with acute abdominal pain followed by rapidly progressive quadriparesis. Two patients had started antiretroviral therapy before the development of symptoms, and one had started antituberculosis therapy. All patients had marked weakness with depressed reflexes, and showed varying degrees of confusion. An initial diagnosis of Guillain-Barré syndrome led to administration of intravenous immunoglobulins in two patients. On testing for porphyria, it was found that two patients had AIP and two VP. Electrophysiological investigations revealed severe mainly motor axonal neuropathy in all. Two patients deteriorated to the point of requiring mechanical ventilation, and one of them died due to complications of critical illness. Haemin was administered to three patients, but the process of obtaining this medication was slow, which delayed the recommended early administration. The surviving patients showed minimal recovery and remained severely disabled. Porphyric neuropathy should always be considered as a differential diagnosis in a patient with an acute neuropathy, especially in SA. Absence of abdominal pain does not exclude the possibility of porphyria, and attacks may be precipitated by antiretroviral and antituberculosis medication. The outcome of our patients was not favourable; specifically, obtaining haemin was a challenge in the state hospital setting

Severe porphyric neuropathy – importance of screening for porphyria in Guillain-Barré syndrome

The hepatic porphyrias are a group of rare metabolic disorders, each of which is associated with a specific enzymatic alteration in the haem biosynthesis pathway. In South Africa (SA), a high incidence of variegate porphyria (VP) is seen as a result of a founder effect, but acute intermittent porphyria (AIP) is also encountered. The development of acute neurovisceral attacks is related to environmental factors, including medications, hormones and diet. A possible manifestation of a severe attack is rapidly progressing quadriparesis, which may mimic Guillain- Barré syndrome. We present four such cases, highlighting that acute porphyria should be considered in the differential diagnosis of Guillain- Barré syndrome. Three patients presented to Steve Biko Academic Hospital, Pretoria, SA, with progressive quadriparesis, and one to a private hospital with acute abdominal pain followed by rapidly progressive quadriparesis. Two patients had started antiretroviral therapy before the development of symptoms, and one had started antituberculosis therapy. All patients had marked weakness with depressed reflexes, and showed varying degrees of confusion. An initial diagnosis of Guillain-Barré syndrome led to administration of intravenous immunoglobulins in two patients. On testing for porphyria, it was found that two patients had AIP and two VP. Electrophysiological investigations revealed severe mainly motor axonal neuropathy in all. Two patients deteriorated to the point of requiring mechanical ventilation, and one of them died due to complications of critical illness. Haemin was administered to three patients, but the process of obtaining this medication was slow, which delayed the recommended early administration. The surviving patients showed minimal recovery and remained severely disabled. Porphyric neuropathy should always be considered as a differential diagnosis in a patient with an acute neuropathy, especially in SA. Absence of abdominal pain does not exclude the possibility of porphyria, and attacks may be precipitated by antiretroviral and antituberculosis medication. The outcome of our patients was not favourable; specifically, obtaining haemin was a challenge in the state hospital setting.http://www.samj.org.zaam2016Chemical PathologyInternal MedicineNeurolog