COVID-19 severity and in-hospital mortality in an area with high HIV prevalence.

Background: HIV infection causes immune dysregulation affecting T-cell and monocyte function, which may alter coronavirus disease 2019 (COVID-19) pathophysiology. Objectives: We investigated the associations among clinical phenotypes, laboratory biomarkers, and hospitalisation outcomes in a cohort of people hospitalised with COVID-19 in a high HIV prevalence area. Method: We conducted a prospective observational cohort study in Tshwane, South Africa. Respiratory disease severity was quantified using the respiratory oxygenation score. Analysed biomarkers included inflammatory and coagulation biomarkers, CD4 T-cell counts, and HIV-1 viral loads (HIVVL). Results: The analysis included 558 patients, of whom 21.7% died during admission. The mean age was 54 years. A total of 82 participants were HIV-positive. People living with HIV (PLWH) were younger (mean age 46 years) than HIV-negative people; most were on antiretroviral treatment with a suppressed HIVVL (72%) and the median CD4 count was 159 (interquartile range: 66-397) cells/µL. After adjusting for age, HIV was not associated with increased risk of mortality during hospitalisation (age-adjusted hazard ratio = 1.1, 95% confidence interval: 0.6-2.0). Inflammatory biomarker levels were similar in PLWH and HIV-negative patients. Detectable HIVVL was associated with less severe respiratory disease. In PLWH, mortality was associated with higher levels of inflammatory biomarkers. Opportunistic infections, and other risk factors for severe COVID-19, were common in PLWH who died. Conclusion: PLWH were not at increased risk of mortality and those with detectable HIVVL had less severe respiratory disease than those with suppressed HIVVL. What this study adds: This study advances our understanding of severe COVID-19 in PLWH.

Post-procedural Bacillus cereus septic arthritis in a patient with systemic lupus erythematosus.

INTRODUCTION: Bacillus species are often considered as contaminants when cultured from clinical samples. Bacillus cereus may be a pathogen in certain circumstances and is known to cause musculoskeletal infections. This report aims to educate clinicians and clinical microbiology laboratories on B. cereus musculoskeletal infections and to heighten awareness that Bacillus species should not always be dismissed as contaminants. CASE PRESENTATION: We report the case of a patient who presented to a tertiary hospital in Pretoria, South Africa, in November 2018 with B. cereus septic arthritis and underlying systemic lupus erythematosus (SLE). The isolate would otherwise have been dismissed as a contaminant had it not been for the crucial interaction between the laboratory and the treating clinicians. To our knowledge, this is the first case report of septic arthritis caused by B. cereus in an SLE patient where the organism was cultured from the joint specimen. Identification of the organism was performed using matrix-assisted laser desorption/ionisation mass spectrometry. MANAGEMENT AND OUTCOME: Definitive treatment was with intravenous vancomycin, continued for four weeks, in addition to arthroscopy and management of the underlying SLE. The patient had a good clinical outcome and regained full mobility. CONCLUSION: Musculoskeletal infections, specifically septic arthritis caused by B. cereus, are exceedingly rare infections. Immune suppression, trauma, prosthetic implants and invasive procedures are important risk factors for B. cereus musculoskeletal infections. Close collaboration with a multi-disciplinary team approach will effect the best outcome for complicated patients with B. cereus infections.

Outbreak of Ralstonia mannitolilytica bacteraemia in patients undergoing haemodialysis at a tertiary hospital in Pretoria, South Africa.

BACKGROUND: Ralstonia species are Gram-negative bacilli of low virulence. These organisms are capable of causing healthcare associated infections through contaminated solutions. In this study, we aimed to determine the source of Ralstonia mannitolilytica bacteraemia in affected patients in a haemodialysis unit. METHODS: Our laboratory noted an increase in cases of bacteraemia caused by Ralstonia mannitililytica between May and June 2016. All affected patients underwent haemodialysis at the haemodialysis unit of an academic hospital. The reverse osmosis filter of the haemodialysis water system was found to be dysfunctional. We collected water for culture at various points of the dialysis system to determine the source of the organism implicated. ERIC-PCR was used to determine relatedness of patient and environmental isolates. RESULTS: Sixteen patients were found to have Ralstonia mannitolilytica bacteraemia during the outbreak period. We cultured Ralstonia spp. from water collected in the dialysis system. This isolate and patient isolates were found to have the identical molecular banding pattern. CONCLUSIONS: All patients were septic and received directed antibiotic therapy. There was 1 mortality. The source of the R. mannitolilytica infection in these patients was most likely the dialysis water as the identical organism was cultured from the dialysis water and the patients. The hospital management intervened and repaired the dialysis water system following which no further cases of R. mannitolilytca infections were detected. A multidisciplinary approach is required to control healthcare associated infections such as these. Routine maintenance of water systems in the hospital is essential to prevent clinical infections with R.mannitolilytica.

Bacterial pathogens in peritoneal dialysis peritonitis: Insights from next-generation sequencing.

BACKGROUND: Peritoneal dialysis (PD) peritonitis is a feared complication of PD, with significant sequelae for the patient. The cause of PD peritonitis is largely due to a single organism (≥75% of cases) and rarely due to multiple organisms. METHODS: In this pilot study, we investigated 25 cases of PD peritonitis with 16S ribosomal RNA (rRNA) next-generation sequencing (NGS) techniques. RESULTS: Total concordance between culture and NGS was noted. In addition, the NGS technique was highly sensitive, identifying 33 different bacteria (including a nonculturable bacterium), compared to 13 bacterial species using culture-based techniques. This was counterbalanced by a lack of specificity with NGS, largely due to the small size of the 16S rRNA gene segment sequenced. CONCLUSIONS: For the clinician, our results suggest that PD peritonitis may often be a polymicrobial disease and that treating a dominant organism may not totally eradicate all bacterial contamination within the peritoneum. For the clinical scientist, additional use of a larger 16S rRNA segment (V5 or V6) is likely to outperform the use of the V4 segment only.