BACKGROUND: Asymptomatic children can be a major reservoir of pharyngeal group A streptococcus (GAS). The role of GAS carriage causing subsequent infections resulting in the manifestation of clinical symptoms, or being associated with transmission to uninfected individuals, is not entirely clear. Furthermore, data on GAS carriage from countries in Africa remain scant with only a few studies reporting carriage OBJECTIVES: We performed a cross-sectional study to determine the prevalence of asymptomatic pharyngeal carriage of group A streptococci in school children in Cape Town. We considered our results in the context of a meta-analysis of data of GAS carriage in Africa METHODS: We conducted a school-based cross-sectional study from 2009 to 2011 in two Cape Town peri-urban communities, enrolling 950 healthy learners. Pharyngeal swabs were obtained from learners and processed at the National Health Laboratory Service (NHLS) microbiology laboratory at Groote Schuur Hospital, Cape Town. Thereafter, we conducted a systematic review through a comprehensive literature search among several sources. Prevalence estimates with 95% confidence intervals (CIs) were determined using a random-effects meta-analysis model RESULTS: GAS was isolated from 31 participants corresponding to a carrier rate of 3% (95% CI 2% - 4%). Combining our results with 18 other studies revealed a pooled prevalence of 9% (95% CI 6% - 11%). Regional pooled rates were similar across southern, eastern and northern Africa, of between 9% (95% CI 6% - 11%) and 11% (95% CI 4% - 21%) while countries within Central Africa had a pooled estimate of 7% (95% CI 5% - 9%). Western Africa had the lowest pooled estimate of 2% (95% CI 1% - 2% CONCLUSION: There was a relatively low rate of carriage of GAS in asymptomatic school children residing in South Africa. Pooled prevalence rates revealed regional differences across the African continent as regards the rate of GAS carriage, with the western and northern African regions having rates of GAS carriage that were lower and higher respectively than those of East, Central and southern African countries, which demonstrated similar rates of carriage

Blood cultures are an important diagnostic and antibiotic stewardship tool to aid in treatment, monitoring and prognosis of patients with infection. This guideline is intended to update our 2010 guideline on the optimal use of blood cultures. Since then, there have been significant changes to the definitions of sepsis, guidance on the number of blood cultures recommended per draw, central and peripheral line blood cultures, advances in mitigating culture contamination, updates on the indications for blood cultures, and guidance on performance of follow-up cultures.

COVID-19 has been reported to affect a variety of organs. We report a case of constrictive pericarditis in a patient who had contracted the SARS-CoV-2 virus. Other possible causes such as tuberculosis and metabolic causes were considered, but excluded by special investigations.

BACKGROUND: In low-resource settings, antimicrobial resistance (AMR) is detected by traditional culture-based methods and ensuring the quality of such services is a challenge. The AMR Scorecard provides laboratories with a technical assessment tool for strengthening the quality of bacterial culture, identification, and antimicrobial testing procedures. OBJECTIVE: To evaluate the performance of the AMR Scorecard in 11 pilot laboratory evaluations in three countries also assessed with the Stepwise Laboratory Quality Improvement Process Towards Accreditation (SLIPTA) checklist METHODS: Pilot laboratory evaluations were conducted in Cameroon, Ethiopia and Kenya between February 2019 and March 2019. Assessors with previous SLIPTA and microbiology experience were trained. Assessors performed the laboratory assessments using the SLIPTA and AMR Scorecard tools. RESULTS: Weaknesses in technical procedures and the quality management systems were identified in all areas and all laboratories. Safety had the highest mean performance score (SLIPTA: 68%; AMR Scorecard: 73%) while management review had the lowest (SLIPTA: 32%; AMR Scorecard: 8%) across all laboratories. The AMR Scorecard scores were generally consistent with SLIPTA scores. The AMR Scorecard identified technical weaknesses in AMR testing, and SLIPTA identified weaknesses in the quality management systems in the laboratories CONCLUSION: Since the AMR Scorecard identified important gaps in AMR testing not detected by SLIPTA, it is recommended that microbiology laboratories use SLIPTA and the AMR Scorecard in parallel when preparing for accreditation. Expanding the use of the AMR Scorecard is a priority to address the need for quality clinical microbiology laboratory services in support of optimal patient care and AMR surveillance.

BACKGROUND: The epidemiology of neonatal and paediatric community-acquired and healthcare-associated bloodstream infections (BSI) at South African (SA) district hospitals is under-researched. OBJECTIVE: Retrospective review of neonatal and paediatric BSI (0 - 13 years) at Khayelitsha District Hospital, Cape Town, SA, over 3 years (1 March 2012 - 28 February 2015). METHODS: We used laboratory, hospital, patient and prescription data to determine BSI rates, blood culture yield and contamination rates, pathogen profile, antimicrobial resistance, patient demographics, BSI outcome and antibiotic prescribing practice. RESULTS: From 7 427 blood cultures submitted, the pathogen yield was low (2.1%, 156/7 427) while blood culture contamination rates were high (10.5%, 782/7 427). Paediatric and neonatal BSI rates were 4.5 and 1.4/1 000 patient days, respectively. Gram-positive BSI predominated (59.3%); Staphylococcus aureus (26.8%) and Escherichia coli (21.6%) were common pathogens. The median patient age was 3 months, with a predominance of males (57.7%) and a 12.8% prevalence of HIV infection. Crude BSI-associated mortality was 7.1% (11/156), the death rate being higher in neonates than in infants and children (6/40 (15.0%) v. 5/116 (4.3%), respectively; p=0.03) and in patients with Gram-negative compared with Gram-positive bacteraemia (6/66 (9.1%) v. 5/89 (5.6%), respectively; p=0.5). Most BSI episodes were community-acquired (138/156; 88.5%), with high levels of extended-spectrum P-lactamase (ESBL) carriage among Klebsiella pneumoniae and E. coli isolates (5/5 (100%) and 8/33 (24.2%), respectively). Antimicrobial management of BSI was inappropriate in 30.6% of cases (45/147), including incorrect empirical antibiotic (46.7%), dual antibiotic cover (33.3%) and inappropriately broad-spectrum antibiotic use (17.8%). CONCLUSIONS: Antimicrobial-resistant pathogens (notably ESBL-producing Enterobacteriaceae) were common in community-acquired BSI. Paediatric clinicians at district hospitals require ongoing training in antibiotic stewardship and blood culture sampling.

Healthcare-associated infection (HAI) is a frequent and serious complication affecting 4 - 8% of hospitalised children and neonates in high-income countries. The burden of HAI in South African (SA) paediatric and neonatal wards is substantial but underappreciated, owing to a lack of HAI surveillance and reporting. Maternal and child health and infection prevention are priority areas for healthcare quality improvement in the National Core Standards programme. Despite increasing recognition in SA, infection prevention efforts targeting hospitalised children and neonates are hampered by health system, institutional and individual patient factors. To ensure safe healthcare delivery to children, a co-ordinated HAI prevention strategy should promote development of infection prevention norms and policies, education, patient safety advocacy, healthcare infrastructure, surveillance and research. We present a framework for SA to develop and expand HAI prevention in hospitalised neonates and children.

BACKGROUND. In 2012, the South African (SA) National Department of Health mandated surveillance of healthcare-associated infection (HAI), but made no recommendations of appropriate surveillance methods. METHODS. Prospective clinical HAI surveillance (the reference method) was conducted at Tygerberg Childrens Hospital, Cape Town, from 1 May to 31 October 2015. Performance of three surveillance methods (point prevalence surveys (PPSs), laboratory surveillance and tracking of antimicrobial prescriptions) was compared with the reference method using surveillance evaluation guidelines. Factors associated with failure to detect HAI were identified by logistic regression analysis. RESULTS. The reference method detected 417 HAIs among 1 347 paediatric hospitalisations (HAI incidence of 31/1000 patient days; 95% confidence interval (CI) 28.2 - 34.2). Surveillance methods had variable sensitivity (S) and positive predictive value (PPV): PPS S = 24.9% (95% CI 21-29.3), PPV = 100%; laboratory surveillance S = 48.4% (95% CI 43.7 - 53.2), PPV = 55.2% (95% CI 50.1-60.2); and antimicrobial prescriptions S = 66.4% (95% CI 61.8 - 70.8%), PPV = 88.5% (95% CI 84.5 - 91.6). Combined laboratory-antimicrobial surveillance achieved superior HAI detection (S = 84.7% (95% CI 80.9 - 87.8%), PPV = 97% (95% CI 94.6 - 98.4%)). Factors associated with failure to detect HAI included patient transfer (odds ratio (OR) 2.0), single HAI event (OR 2.8), age category 1 - 5 years (OR 2.1) and hospitalisation in a general ward (OR 2.3). CONCLUSIONS. Repeated PPSs, laboratory surveillance and/or antimicrobial prescription tracking are feasible HAI surveillance methods for low-resource settings. Combined laboratory-antimicrobial surveillance achieved the best sensitivity and PPV. SA paediatric healthcare facilities should individualise HAI surveillance, selecting a method suited to available resources and practice context.

BACKGROUND: The benchmark for contaminated blood cultures (BCs) is 3%. The South African (SA) guideline aims to optimise BC yield and reduce contamination. Data on BC collection practices in SA since the publication of the 2010 SA guideline are lacking. OBJECTIVE: To evaluate compliance with the national guideline for the optimal use of BCs and determine the BC contamination rate at a local district hospital. METHOD: An audit of compliance with 22 BC standards was conducted at a district hospital in Cape Town, SA. Standards were evaluated by reviewing clinical and laboratory data and by a clinician questionnaire. RESULTS: Of the 425 BCs reviewed, 12.5% had positive growth, and 4.5% grew contaminants. Only 33% of BC bottles contained the recommended fill volume of 8 - 10 mL, and 96.9% of patients had a single BC within a 24-hour period. Of all the BCs, only 7.8% had a combined blood volume of at least 20 mL. The yield of pathogens in BCs collected after antibiotic exposure was 4.9% compared with 7.5% for those cultures with no prior antibiotic exposure (p=0.3). The overall median needle-to-incubator transport time was 11 hours 25 minutes. CONCLUSION: The BC contamination rate was high and compliance with most standards was variable or not met. The findings may not be generalisable to other hospitals, and we recommend that each institution reviews its own BC practices. Recommendations made to hospital staff included a re-audit following implementation of these recommendations.

Infection control has been identified as one of the key interventions in controlling the threat of antibiotic resistance. Reducing the transmission of multidrug-resistant organisms (MDROs) reduces the need for broad-spectrum antibiotics in particular, while interventions that decrease the risk of infection have an impact on the use of any antibiotic. Hand hygiene remains the cornerstone of decreasing the transmission of MDROs. Alcohol-based hand rubs are a cheap, effective and convenient means of performing hand hygiene. Patients colonised or infected with MDROs should be placed on contact precautions, although implementation remains challenging in resource-limited environments. Screening for certain MDROs may play a role in curbing transmission of these organisms. If implemented, screening must be part of a comprehensive infection control strategy. In resource-limited settings, the costs and potential benefits of screening programmes need to be carefully weighed up. Care bundles have been shown to reduce the incidence of common healthcare-associated infections, including catheter-associated urinary tract infection, ventilator-associated pneumonia, central line-associated bloodstream infection and surgical site infection. These bundles are relatively inexpensive, and can play an important role in reducing antibiotic use and improving clinical outcomes.

BACKGROUND: Diarrhoea due to gastrointestinal infections is a significant problem facing the South African (SA) healthcare system. Infections can be acquired both from the community and from the hospital environment itself, the latter acting as a reservoir for potential pathogenic bacteria. OBJECTIVES: To examine the prevalence of a panel of potential diarrhoea-causing bacteria in patients attending a tertiary healthcare facility in Cape Town, SA. METHODS: Polymerase chain reaction (PCR) primers specific for Clostridium difficile, Shigella spp., Salmonella spp., Klebsiella oxytoca, enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC/EHEC), Staphylococcus aureus, enterotoxigenic Bacteroides fragilis and Campylobacter spp. were used to screen total bacterial genomic DNA extracted from stool samples provided by 156 patients with diarrhoea attending Groote Schuur Hospital, Cape Town, SA. RESULTS: C. difficile was the most frequently detected pathogen (16% of cases) in the 21 - 87-year-old patient range, but was not present in samples from the 16 - 20-year-old range. K. oxytoca (6%), EPEC/EHEC strains (9%) and S. aureus (6%) were also detected. The remaining pathogens were present at low frequencies (0 - 2.9%), and the occurrence of mixed infections was 5%. The majority of non-C. difficile-related diarrhoeas were community acquired. CONCLUSION: C. difficile was the main cause of infectious diarrhoea in the sampled patients, while K. oxytoca and EPEC/EHEC strains were present as relatively minor but potentially significant pathogens.

ABSTRACT BACKROUND: The increasing rates of antimicrobial resistance observed in the nosocomial pathogen Klebsiella pneumoniae are of major public health concern worldwide. OBJECTIVES: To describe the antibiotic susceptibility profiles of K. pneumoniae isolates from bacteraemic patients submitted by sentinel laboratories in five regions of South Africa from mid-2010 to mid-2012. Molecular methods were used to detect the most commonly found extended-spectrum beta-lactamase (ESBL) and carbapenemase resistance genes. METHODS: Thirteen academic centres serving the public healthcare sector in Gauteng, KwaZulu-Natal, Free State, Limpopo and Western Cape provinces submitted K. pneumoniae isolates from patients with bloodstream infections. Vitek 2 and MicroScan instruments were used for organism identification and susceptibility testing. Multiplex polymerase chain reactions (PCRs) were used to detect blaCTX-M, blaSHV and blaTEM genes in a proportion of the ESBL isolates. All isolates exhibiting reduced susceptibility to carbapenems were PCR tested for blaKPC and blaNDM-1 resistance genes. RESULTS: Overall, 68.3% of the 2 774 isolates were ESBL-positive, showing resistance to cefotaxime, ceftazidime and cefepime. Furthermore, 46.5% of all isolates were resistant to ciprofloxacin and 33.1% to piperacillin-tazobactam. The major ESBL genes were abundantly present in the sample analysed. Most isolates (95.5%) were susceptible to the carbapenems tested, and no isolates were positive for blaKPC or blaNDM1 There was a trend towards a decrease in susceptibility to most antibiotics. CONCLUSION: The high proportion of ESBL-producing K. pneumoniae isolates observed, and the prevalence of ESBL genes, are of great concern. Our findings represent a baseline for further surveillance in SA, and can be used for policy and treatment decisions.

BACKGROUND: Chronic otorrhoea is difficult to treat, with treatment in South Africa (SA) being protocol driven and generally initiated at the primary healthcare level. There is a lack of local studies that focus on the bacteriology and antimicrobial sensitivities of chronic otorrhoea, which underpins the management advice offered. AIMS: To determine the microbiological profile and antimicrobial susceptibility of patients with chronic otorrhoea and the validity of the Department of Health's (DoH) current guideline. METHODS: We conducted a prospective study at Groote Schuur Hospital from 2005 to 2009. We included patients with chronic otorrhoea classified as either otitis media or otitis externa, according to our definitions. Pus swabs were taken, from which microorganisms were cultured and tested for antimicrobial susceptibility. RESULTS: Of 79 patients with otorrhoea, 50 had otitis media, 21 had otitis externa and the condition was not determined in 8 patients. The most common organism isolated with otitis media was Proteus mirabilis (18/50; 36%) and with otitis externa, Pseudomonas aeruginosa (7/21; 33%). Otorrhoea had a different microbial spectrum compared with international reports, with methicillin-resistant Staphylococcus aureus infection in a single patient. The organisms isolated were susceptible mainly to fluoroquinolones (96%) and aminoglycosides (81%). CONCLUSION: Amoxicillin is a poor choice of antibiotic due to its low sensitivity, which calls into question the current DoH guideline for otorrhoea. Antimicrobial treatment protocols should be based on local data and be revisited from time to time. This study suggests that, should first-line treatment fail, an antibiotic with Gram-negative cover, e.g. a topical fluoroquinolone, should be considered

BACKGROUND AND OBJECTIVES: The aim of this study is to report the incidence of Clostridium difficile-associated disease (CDAD) in a tertiary-care hospital in South Africa and to identify risk factors, assess patient outcomes and determine the impact of the hypervirulent strain of the organism referred to as North American pulsed-field type 1 (NAP1). METHODS: Adults who presented with diarrhoea over a period of 15 months were prospectively evaluated for CDAD using stool toxin enzyme immunoassay (EIA). Positive specimens were evaluated by PCR. Patient demographics, laboratory parameters and outcomes were analysed. RESULTS: CDAD was diagnosed in 59 (9.2%) of 643 patients (median age 39 years, IQR 30 - 55). Thirty-four (58%) were female. Recent antibiotic exposure was reported in 39 (66%), 27 (46%) had been hospitalised within 3 months, and 14 (24%) had concomitant inflammatory bowel disease (IBD). Nineteen (32%) had community-acquired CDAD (CA-CDAD). The annual incidence of hospital-acquired CDAD (HA-CDAD) was 8.7 cases/10 000 hospitalisations. Two cases of the hypervirulent strain NAP1 were identified. Seven (12%) patients underwent colectomy (OR 6.83; 95% CI 2.41 - 19.3). On logistic regression, only antibiotic exposure independently predicted for CDAD (OR 2.9; 95% CI 1.6 - 5.1). Three (16%) cases of CA-CDAD reported antibiotic exposure (v. 90% of HA-CDAD, p<0.0001). Twelve (86%) patients had concomitant IBD (p<0.0001 v. HA-CDAD). CA-CDAD was significantly associated with antibiotic exposure (OR 0.04, 95% CI 0.01 - 0.24) and IBD (OR 9.6, 95% CI 1.15 - 79.8). CONCLUSION: The incidence of HA-CDAD in the South African setting is far lower than that reported in the West. While antibiotic use was a major risk factor for HA-CDAD, CA-CDAD was not associated with antibiotic therapy. Concurrent IBD was a predictor of CA-CDAD.