Purpose: There is growing concern about the increasing prevalence of Listeria monocytogenes associated with foodborne outbreaks. Data concerning the prevalence and epidemiology of L. monocytogenes in South Africa are lacking. To prevent, investigate and control Listeria outbreaks, molecular epidemiological data are critical for understanding strain relatedness and defining source attribution. This present study describes the first whole-genome sequencing data for L. monocytogenes isolates from South Africa. Methods & Materials: A cluster of human cases of L. monocytogenes was recently reported from the Western Cape Province (WCP) of South Africa. This initiated our inaugural whole-genome sequencing (WGS) analysis of L. monocytogenes. To date, 11 isolates have been analyzed; WCP [n=9], Gauteng Province (GP) [n=1] and Eastern Cape Province (ECP) [n=1]. For WGS analysis, raw sequencing data generated on Illumina MiSeq equipment (2 x 300 paired-end sequencing runs) was analyzed using tools available in the CLC Genomics Workbench Software; trimmed reads were assembled using the ‘De novo Assembly Tool’. Assembled WGS data was analyzed using bioinformatics tools and on-line analysis pipelines available at the Center for Genomic Epidemiology (CGE), Technical University of Denmark (http://cge.cbs.dtu.dk/services/). Results: Single nucleotide polymorphism (SNP) analysis separated our 11 isolates into 6 branches of a SNP phylogenetic tree. In particular, SNP analysis determined that the cluster of WCP isolates was not the result of a single strain, but rather that several strains were involved. Multi-locus sequence typing (MLST) data concurred with SNP results in differentiating the isolates. MLST subtype data were as follows: ST6 (n=4, WCP), ST1 (n=2, WCP), ST876 (n=2, WCP), ST54 (n=1, WCP), ST3 (n=1, GP), ST820 (n=1, ECP). In particular, our largest group was associated with MLST subtype ST6, a subtype commonly associated with unfavourable outcomes in patients. Conclusion: Analysis of WGS data using bioinformatics tools and on-line analysis pipelines at the CGE provided a single, rapid and cost-effective approach to investigate the molecular epidemiology of L. monocytogenes. This study has initiated a larger surveillance project for L. monocytogenes in South Africa. In future, all South African L. monocytogenes isolates will routinely be investigated using WGS.

Background: Salmonella species are gram negative bacilli with over 2600 serotypes and a worldwide distribution. Non-typhoidal Salmonella (NTS) typically causes self-limiting gastroenteritis, but may become invasive. In sub-Saharan Africa invasive NTS disease is associated with a high mortality, associated with malnutrition, malaria and human immunodeficiency virus (HIV) co-infection. Meningitis due to NTS is a rare complication, with mortality rates over 40% in children. We report three cases of NTS meningitis in paediatric patients in Cape Town (Note: two more cases have been identified). Methods & Materials: A five-year review of NTS cultured from cerebrospinal fluid (CSF) at the Division of Medical Microbiology, Groote Schuur Hospital was performed. This is a tertiary academic microbiology laboratory. The National Health Laboratory Service (NHLS) laboratory information system was searched from 1 July 2010 to 30 June 2015. Retrospective clinical reviews were conducted for these cases including patient history, clinical features, risk factors, treatment and outcomes. Results: From all CSF cultures sent to GSH Microbiology laboratory (n=41865), three cases of NTS meningitis were identified. All three Salmonella meningitis cases were in infants less than one year old. One infant was Zimbabwean with a travel history. All cases were HIV-uninfected: one child was HIV exposed. NTS was isolated from both CSF and blood culture in 2 cases, no blood culture was done on the third. Salmonella enterica serotype Enteritidis (Salmonella Enteritidis) was cultured from two cases and Salmonella Heidelberg from the third. All isolates were susceptible to all antimicrobials tested. One patient died within 72 hours of admission; the remaining two developed neurological complications, including hydrocephalus, hemiplegia and cerebral infarcts. Conclusion: NTS meningitis should be considered in infants if gram negative bacilli are observed in CSF. The prevalence of NTS meningitis in South Africa appears to be low. A third-generation cephalosporin (Ceftriaxone/Cefotaxime) remains the empiric treatment for meningitis. The duration of treatment for gram negative meningitis is usually 21 days. For NTS meningitis at least 4 weeks of therapy may be indicated to prevent relapses. In view of the poor prognosis and high risk of relapse the use of combination therapy with a cephalosporin and fluoroquinolone, which has enhanced intracellular activity, may be required.

SUMMARY In 2005, over 600 clinically diagnosed typhoid fever cases occurred in South Africa, where an outbreak had been previously described in 1993. Case-control and molecular investigations, including Salmonella enterica serovar Typhi (S. Typhi) isolates from that area from 1993, 2005 and later, were undertaken. Controls were significantly older than cases (P=0·003), possibly due to immunity from previous infection, and a significantly larger proportion had attended a gathering (P=0·035). Exposure to commercial food outlets and person-to-person transmission was not significant. Pulsed-field gel electrophoresis and multi-locus tandem repeat analysis revealed common clusters of S. Typhi strains identified in 1993 and 2005 as well as in 2007 and 2009. This outbreak probably occurred in a non-immune population due to faecally contaminated water. S. Typhi strains appeared to be related to strains from 1993; failure to address unsafe water may lead to further outbreaks in the area if the current population immunity wanes or is lost.

Background: In Sub-Saharan Africa, non-typhoidal salmonellae (NTS) are an important cause of bacteraemia, with case-fatality ratios (CFR) amongst hospitalized children ranging from 4%-27%. Methods: NTS isolated from normally-sterile sites from January 2004 through December 2008 were reported to a national, laboratory-based surveillance system. In-hospital outcome, HIV infection status and other clinical data were collected at sentinel sites. Incidence rates for 2007 amongst HIV-infected and–uninfected children) 5 years were calculated, assuming that the age-specific HIV prevalence amongst tested children was similar to those not tested for HIV. Risk factors for death were evaluated using logistic regression. Nosocomial infection was defined as infection identified from specimens collected > 2 days after admission. Results: The highest incidence of NTS was amongst children aged < 1 year (19.8 per 100,000) and 1 year old children (6.2 per 100,000) as compared to older children (1.1 per 100,000 for 2 to 5 years old age group). The overall incidence was 88.3 (per 100,000) amongst HIV-infected children and 2.7 (per 100,000) amongst HIV-uninfected children. HIV-infected children with invasive NTS infection had a 3.4-fold increased odds (95% confidence interval [CI95%] 1.9–6.3) of dying compared to HIV-uninfected children (30%, (50/166) HIV-infected versus 9%, (10/112) HIV-uninfected, p < 0.001). The CFR was higher amongst patients aged < 1 year (22%, 88/399) compared to those aged 1-5 years (16%, 40/248) (OR 1.5 CI95% 1.00–2.2, p = 0.066). CFR varied by province: 6% (7/111) Western Cape, 20% (64/319) Gauteng, 24% (31/128) KwaZulu-Natal and 29% (26/91) other provinces, p < 0.001. Nosocomial infections accounted for 19% (96/496) of infections and were associated with a 1.8-fold (CI95% 1.1– 3.0) higher risk of death compared to community-acquired infections (CFR 29% (27/94) nosocomial versus 19% (73/392) community-acquired, p = 0.030). On multivariable analysis, controlling for province, HIV-infected children with invasive NTS had a 3 times greater odds of death as compared to HIV-uninfected children p = 0.002 (OR 3.0 CI95% 1.7–5.5). Conclusion: The incidence of NTS was highest in children aged < 1 year and HIV-infected children. HIV-infected children were also at increased risk of death. Access to prevention of mother-to-child transmission, HIV testing and highly active antiretroviral therapy should be prioritised. Abstracts for SupplementInternational Journal of Infectious DiseasesVol. 14Preview Full-Text PDF Open Archive