Epidemiology and risk factors for candidaemia at Chris Hani Baragwanath hospital (2009-2010)

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, in fulfillment for the requirements for the degree of Master of Medicine in Microbiology. Johannesburg, 2017Background Invasive Candida infections (ICI) have emerged as an important cause of increased morbidity and mortality in specific patient populations in recent years. Multiple risk factors coupled with changes in epidemiology have made clinical management of these patients challenging. A laboratory-based surveillance project, Tracking Resistance to Antifungal drugs for Candida species in South Africa (TRAC-SA) was conducted at Chris Hani Baragwanath Hospital (CHBH) from 2009 to 2010 and allowed for collection of laboratory information related to episodes of candidaemia, delineation of the situation at the hospital and distribution of information to relevant stakeholders to help make informed clinical decisions. Objective Determine the clinical epidemiology and risk factors for bloodstream Candida infection at CHBH over an 18-month period Methods A retrospective, cross-sectional analysis was carried out on cases of blood culture-confirmed candidaemia from inpatients from 1 February 2009 until 31 August 2010. These cases were identified from the TRAC-SA database, inpatient files were traced and clinical data recorded on a standard case report form. Additional laboratory data of selected tests done within 72 hours of the initial blood culture were obtained from the National Laboratory Health Service Corporate Data Warehouse (CDW). Results A total of 167 episodes of candidaemia were identified during the study period with an incidence of 2.09 per 1000 admissions. The distribution of episodes occurred among 55 children (33%), 41 adults (25%) and 71 neonates (43%). The overall species distribution was Candida species other than C. albicans (98/167, 58.7%) and C. albicans (69/167, 41.3%). Candida species other than C. albicans comprised mainly of C. parapsilosis (73/167, 43.7%), C. glabrata (10.2 %, 17/167) and other species combined including C. tropicalis and C. krusei (8/167, 4.7%). Factors associated with C. albicans (versus Candida species other than C. albicans) infection included older age, use of 2 or more antibiotics, use of broad spectrum antibiotics specifically meropenem, aminoglycosides, vancomycin, co-trimoxazole and mechanical ventilation (p < 0.001). The overall case-fatality was 59/163 (35.3%). The highest case fatality was noted among adults with C. albicans infection, i.e. 15/22 (68.18%). Significant risk factors associated with in-hospital mortality were use of central lines, urinary catheters, total parenteral nutrition, 2 or more antibiotics, beta lactam - beta lactamase inhibitors, proton pump inhibitors, aminoglycoside and abdominal surgery (p < 0.01). Of the C. parapsilosis isolates tested, 40 (57. 9%) tested non-susceptible to fluconazole. Risk factors associated with fluconazole resistance included neonatal age, involvement of the respiratory system, mechanical ventilation, chemotherapy, use of a prior antifungal agent and use of 2 or broader spectrum antibiotics (p<0.01). Of 71 neonates, 16 (22.5%) received empiric antifungals, in comparison to children (5/55, 9.0%) and adults (4/41, 9.7%) (p = 0.272). Conclusion CHBH had a high incidence of candidaemia with a predominance of Candida species other than C. albicans especially in the neonate age group. Risk stratification of in-patients is of paramount importance in choice of empiric antifungal drug due to the differing azole resistance patterns observed.MT201

Prevalence and trends of staphylococcus aureus bacteraemia in hospitalized patients in South Africa, 2010 to 2012: laboratory-based surveillance mapping of antimicrobial resistance and molecular epidemiology.

CAPRISA, 2015.Abstract available in pdf

Systemic shigellosis in South Africa

BACKGROUND: Systemic disease due to shigellae is associated with human immunodeficiency virus (HIV), malnutrition, and other immunosuppressed states. We examined the clinical and microbiologic characteristics of systemic shigellosis in South Africa, where rates of HIV infection are high. METHODS: From 2003 to 2009, 429 cases of invasive shigellosis were identified through national laboratory-based surveillance. At selected sites, additional information was captured on HIV serostatus and outcome. Isolates were serotyped and antimicrobial susceptibility testing performed. RESULTS: Most cases of systemic shigellosis were diagnosed on blood culture (408 of 429 cases; 95%). HIV prevalence was 67% (80 of 120 cases), highest in patients aged 5–54 years, and higher among females (55 of 70 cases; 79%) compared with males (25 of 48 cases; 52%; P 5 .002). HIV-infected people were 4.1 times more likely to die than HIV-uninfected cases (case-fatality ratio, 29 of 78 HIV-infected people [37%] vs 5 of 40 HIV-uninfected people [13%]; P 5 .008; 95% confidence interval [CI], 1.5–11.8). The commonest serotype was Shigella flexneri 2a (89 of 292 serotypes [30.5%]). Pentavalent resistance occurred in 120 of 292 isolates (41.1%). There was no difference in multidrug resistance between HIV-infected patients (33 of 71 [46%]) and uninfected patients (12 of 33 [36%]; 95% CI, .65–3.55). CONCLUSIONS: Systemic shigellosis is associated with HIV-infected patients, primarily in older girls and women, potentially due to the burden of caring for sick children in the home; interventions need to be targeted here. Death rates are higher in HIV-infected versus uninfected individuals.The US Agency for International Development’s Antimicrobial Resistance Initiative, transferred via a cooperative agreement (grant U60/CCU022088) from the Centers for Disease Control and Prevention (CDC), Atlanta, Georgia. For 2007–2009, it was supported by the Departments of Health and Human Services (HHS) CDC, the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (NCHHSTP), the Global AIDS Program (GAP) Cooperative Agreement (U62/PSO022901). P. C.-G. and S. M. are funded through grant U60/CCU022088.http://cid.oxfordjournals.org

Federation of Infectious Diseases Societies of Southern Africa guideline : recommendations for the detection, management and prevention of healthcare-associated Candida auris colonisation and disease in South Africa

Candida auris has been detected at almost 100 South African hospitals, causing large outbreaks in some facilities, and this pathogen now accounts for approximately 1 in 10 cases of candidaemia. The objective of this guideline is to provide updated, evidence-informed recommendations outlining a best-practice approach to prevent, diagnose and manage C. auris disease in public- and private-sector healthcare settings in South Africa. The 18 practical recommendations cover five focus areas: laboratory identification and antifungal susceptibility testing, surveillance and outbreak response, infection prevention and control, clinical management and antifungal stewardship.The South African Society for Clinical Microbiology and the Federation of Infectious Diseases Societies of Southern Africa.https://sajid.co.za/index.php/sajidpm2020School of Health Systems and Public Health (SHSPH

Antimicrobial susceptibility patterns of selected bacteraemic isolates from South African public sector hospitals, 2010

We report on antimicrobial susceptibility surveillance data for six key bloodstream pathogens (Escherichia coli, Klebsiella pneumoniae, Enterobacter spp., Pseudomonas aeruginosa, Acinetobacter baumannii and Staphylococcus aureus) identified in public sector hospitals in South Africa during 2010. Major findings include the accelerated emergence of carbapenem resistance among K. pneumoniae and Enterobacter species, with overall susceptibility rates of 98% and 96% for ertapenem, and above 99% for meropenem and imipenem. Levels of resistance among P. aeruginosa and A. baumannii remain high in all centres, with few changes since 2009. Large decreases in piperacillin-tazobactam susceptibility rates were noted at three institutions, probably related to methodological issues. S. aureus remains a major pathogen countrywide, with between 30-60% of isolates resistant to cloxacillin [methicillin-resistant S. aureus (MRSA)]. Ongoing surveillance for antimicrobial resistance is vital, and the use of a centralised data extraction system may aid in this.http://www.sajei.co.za/index.php/SAJE

Epidemiology of Serotype 1 Invasive Pneumococcal Disease, South Africa, 2003–2013

In South Africa, 7-valent pneumococcal conjugate vaccine (PCV) was introduced in April 2009 and replaced with 13-valent PCV in April 2011. We describe the epidemiology of serotype 1 Streptococcus pneumoniae disease during the pre- and post-PCV eras (2003–2013). Using laboratory-based invasive pneumococcal disease (IPD) surveillance, we calculated annual incidences, identified IPD clusters, and determined serotype 1–associated factors. Of 46,483 IPD cases, 4,544 (10%) were caused by serotype 1. Two clusters of serotype 1 infection were detected during 2003–2004 and 2008–2012, but incidence decreased after 2011. Among children <5 years of age, those who had non–serotype 1 IPD had shorter hospital stays, fewer cases of penicillin-nonsusceptible disease, and lower HIV prevalence and in-hospital death rates than did those with serotype 1 IPD; similar factors were noted for older patients. Serotype 1 IPD had distinctive clinical features in South Africa, and annual incidences fluctuated, with decreases noted after the introduction of PCV13

Antibiotics MIC₅₀, MIC₉₀ and breakpoints for 2 709 <i>S</i>. <i>aureus</i> isolates.

<p>Antibiotics MIC₅₀, MIC₉₀ and breakpoints for 2 709 <i>S</i>. <i>aureus</i> isolates.</p