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A nosocomial outbreak of disease involving 5 patients, 4 of whom died, occurred in South Africa during September-October 2008. The first patient had been transferred from Zambia to South Africa for medical management. Three cases involved secondary spread of infection from the first patient, and 1 was a tertiary infection. A novel arenavirus was identified. The source of the first patient's infection remains undetermined. [ABSTRACT FROM AUTHOR]

We describe a case of neoehrlichiosis in an immunocompetent child with acute febrile illness in South Africa. Neoehrlichiosis was diagnosed by PCR on 16S rDNA from bone marrow aspirate. Phylogenetic analysis indicated an organism closely related to Candidatus Neoehrlichia. Clinicians should be aware of possible ehrlichiosis even in immunocompetent patients.

Background: The National Institute for Communicable Diseases (NICDs) of South Africa (SA) provides technical support to healthcare workers (HCWs) with regard to infectious diseases through the NICD clinician hotline. Queries to the hotline are often about rabies prophylaxis. An analysis of these queries may help to identify knowledge gaps amongst HCWs regarding prevention of rabies in humans in SA., Methods: A retrospective descriptive review was conducted to analyse rabies post-exposure prophylaxis (PEP) queries received by the NICD from 01 January 2016 to 31 December 2019., Results: A total of 4655 queries were received by the NICD clinician hotline for the study period, of which 2461 pertained to rabies PEP (52.87%). The largest number of calls were placed by HCWs ( n = 2313/2437; 94.9%). Queries originated mainly from Gauteng ( n = 912/2443; 37.3%) and KwaZulu-Natal ( n = 875/2443; 35.8%) provinces. A total of 50 different types of animals were related to exposures involving humans. Dogs (67.7%) and cats (11.8%) were the animals most frequently reported and exposure category III was most common (88.6%). Approximately equal numbers of callers were advised active management of administering rabies PEP and conservative management of withholding PEP. This did not seem to be affected by the exposure category related to the call., Conclusion: This analysis shows the ongoing demand by HCWs for technical support regarding patient management following potential exposure to rabies. Gaps in HCWs rabies knowledge provide unique learning points on guiding training to achieve the goal of eliminating dog-mediated human rabies deaths by 2030., Competing Interests: The authors declare that they have no financial or personal relationships that may have inappropriately influenced them in writing this article., (© 2022. The Authors.)

Background: We describe the epidemiology of COVID-19 in South Africa following importation and during implementation of stringent lockdown measures., Methods: Using national surveillance data including demographics, laboratory test data, clinical presentation, risk exposures (travel history, contacts and occupation) and outcomes of persons undergoing COVID-19 testing or hospitalised with COVID-19 at sentinel surveillance sites, we generated and interpreted descriptive statistics, epidemic curves, and initial reproductive numbers (Rt)., Findings: From 4 March to 30 April 2020, 271,670 SARS-CoV-2 PCR tests were performed (462 tests/100,000 persons). Of these, 7,892 (2.9%) persons tested positive (median age 37 years (interquartile range 28-49 years), 4,568 (58%) male, cumulative incidence of 13.4 cases/100,000 persons). Hospitalization records were found for 1,271 patients (692 females (54%)) of whom 186 (14.6%) died. Amongst 2,819 cases with data, 489/2819 (17.3%) travelled internationally within 14 days prior to diagnosis, mostly during March 2020 (466 (95%)). Cases diagnosed in April compared with March were younger (median age, 37 vs. 40 years), less likely female (38% vs. 53%) and resident in a more populous province (98% vs. 91%). The national initial R t was 2.08 (95% confidence interval (CI): 1.71-2.51)., Interpretation: The first eight weeks following COVID-19 importation were characterised by early predominance of imported cases and relatively low mortality and transmission rates. Despite stringent lockdown measures, the second month following importation was characterised by community transmission and increasing disease burden in more populous provinces., Competing Interests: KMM, PNN, JE, GN, YP, LE, DM, AMS, KS, MM, KM, NW, TM, JK, TK, WJ, LHB, SM, ST, SW declare no competing interests. AvG reports receipt of funding and equipment to the NICD to support surveillance for SARS-CoV-2 from the South African Medical Research Committee (funding), Wellcome Trust (funding), European Union, Germany (equipment), the Jack Ma Foundation (Allibaba) (testing equipment and reagents), the Centres for Disease Control, Atlanta (funding), the EDCTP (funding), the Africa CDC (funding) and the Fleming Fund (funding). CC reports grants from US CDC, grants from Wellcome Trust, grants from South Africa MRC during the conduct of the study and grants from Sanofi Pasteur outside the submitted work; NPG reports grants from NIH, grants from US CDC, grants from CDC Foundation, grants from Bill and Melinda Gates Foundation, grants from NHLS Research Trust, grants from UK MRC (JGHT scheme) all outside the submitted work. The findings and conclusions in this manuscript are those of the authors and do not necessarily represent the official position of the authors’ affiliated institutions or funding agencies., (© 2021 The Authors.)

No abstract available.

Background: An outbreak of listeriosis was identified in South Africa in 2017. The source was unknown., Methods: We conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type Listeria monocytogenes isolates. A case was defined as laboratory-confirmed L. monocytogenes infection during the period from June 11, 2017, to April 7, 2018., Results: A total of 937 cases were identified, of which 465 (50%) were associated with pregnancy; 406 of the pregnancy-associated cases (87%) occurred in neonates. Of the 937 cases, 229 (24%) occurred in patients 15 to 49 years of age (excluding those who were pregnant). Among the patients in whom human immunodeficiency virus (HIV) status was known, 38% of those with pregnancy-associated cases (77 of 204) and 46% of the remaining patients (97 of 211) were infected with HIV. Among 728 patients with a known outcome, 193 (27%) died. Clinical isolates from 609 patients were sequenced, and 567 (93%) were identified as sequence type 6 (ST6). In a case-control analysis, patients with ST6 infections were more likely to have eaten polony (a ready-to-eat processed meat) than those with non-ST6 infections (odds ratio, 8.55; 95% confidence interval, 1.66 to 43.35). Polony and environmental samples also yielded ST6 isolates, which, together with the isolates from the patients, belonged to the same core-genome multilocus sequence typing cluster with no more than 4 allelic differences; these findings showed that polony produced at a single facility was the outbreak source. A recall of ready-to-eat processed meat products from this facility was associated with a rapid decline in the incidence of L. monocytogenes ST6 infections., Conclusions: This investigation showed that in a middle-income country with a high prevalence of HIV infection, L. monocytogenes caused disproportionate illness among pregnant girls and women and HIV-infected persons. Whole-genome sequencing facilitated the detection of the outbreak and guided the trace-back investigations that led to the identification of the source., (Copyright © 2020 Massachusetts Medical Society.)

An atypical case of Crimean-Congo haemorrhagic fever is presented. The diagnosis of the case in the presence of several comorbidities was complicated and illustrates the importance of maintaining a high index of suspicion for viral haemorrhagic fever in cases presenting with multisystem disease and an epidemiological history that could present opportunities for exposure to a haemorrhagic fever virus.

A lack of surveillance and diagnostics for zoonotic diseases in rural human clinics limits clinical awareness of these diseases. We assessed the prevalence of nine zoonotic pathogens in a pastoral, low-income, HIV-endemic community bordering wildlife reserves in South Africa. Two groups of participants were included: malaria-negative acute febrile illness (AFI) patients, called febrilers, at three clinics (n = 74) and second, farmers, herders, and veterinary staff found at five government cattle dip-tanks, called dip-tanksters (n = 64). Blood samples were tested using one PCR (Bartonella spp.) and eight antibody-ELISAs, and questionnaires were conducted to assess risk factors. Seventy-seven percent of febrilers and 98% of dip-tanksters had at least one positive test. Bartonella spp. (PCR 9.5%), spotted fever group (SFG) Rickettsia spp. (IgM 24.1%), Coxiella burnetii. (IgM 2.3%), and Leptospira spp. (IgM 6.8%) were present in febrilers and could have been the cause of their fever. Dip-tanksters and febrilers had evidence of past infection to Rickettsia spp. (IgG 92.2% and 63.4%, respectively) and C. burnetii (IgG 60.9% and 37.8%, respectively). No Brucella infection or current Bartonella infection was found in the dip-tanksters, although they had higher levels of recent exposure to Leptospira spp. (IgM 21.9%) compared to the febrilers. Low levels of West Nile and Sindbis, and no Rift Valley fever virus exposure were found in either groups. The only risk factor found to be significant was attending dip-tanks in febrilers for Q fever (p = 0.007). Amoxicillin is the local standard treatment for AFI, but would not be effective for Bartonella spp. infections, SFG rickettsiosis, Q fever infections, or the viral infections. There is a need to revise AFI treatment algorithms, educate medical and veterinary staff about these pathogens, especially SFG rickettsiosis and Q fever, support disease surveillance systems, and inform the population about reducing tick and surface water contact.

A suspicion on West Nile virus (WNV) in Serbia was first reported in 1972 by a seroprevalence study, after which no data were available for four decades. We report full sequence of the isolate obtained for the first time from a human sample in Serbia. The closest clustering was obtained with lineage 2 WNV identified in Greece in 2010. Since WNV lineage 2 emerged in Europe in 2004, a cocirculation of lineages 1 and 2-as observed in Hungary and Italy-cannot be excluded. The reinforcement of surveillance will be required to investigate the possible cocirculation of the two lineages and the burden of WNV in the local population.

Viral haemorrhagic fevers (VHFs) include a diverse array of diseases caused by a broad range of viruses transmitted from various animal hosts and originating from almost all the continents in the world. These are potentially fatal and highly transmissible diseases without specific treatments or prophylactic vaccines. As has been demonstrated during the Ebola virus disease outbreak in West Africa, the consequences of VHFs are not limited to specific countries - they may become epidemic, and may have considerable economic impact and disrupt local public health and social service structures. Intensive public health intervention is necessary to contain these diseases. Here we provide a concise overview of the VHFs that are of current public health importance to South Africa.

Notified malaria cases in South Africa (SA) decreased significantly over the past 14 years, from over 60 000 in the 1999/2000 malaria season to less than 13 000 in 2013/2014. However, the past two seasons have seen increases in both local and imported cases. Mozambique contributes the highest number of imported cases in SA. This update provides recommendations for malaria treatment and prevention (in travellers and residents) for 2015.

Canine rabies is enzootic throughout Sub-Saharan Africa, including the Republic of South Africa. Historically, in South Africa the coastal provinces of KwaZulu-Natal and Eastern Cape were most affected. Alarmingly, outbreaks of canine rabies have been increasingly reported in the past decade from sites where it has previously been under control. From January 2010 to December 2011, 53 animal rabies cases were confirmed; these were mostly in domestic dogs from southern Johannesburg, which was previously considered to be rabies free. In addition, one case was confirmed in a 26-month old girl who had been scratched by a pet puppy during this period. The introduction of rabies into Gauteng Province was investigated through genetic analysis of rabies positive samples confirmed during the outbreak period. In addition, the nucleotide sequences of incidental cases reported in the province for the past ten years were also included in the analysis. It was found that the recent canine rabies outbreak in the Gauteng Province came from the introduction of the rabies virus from KwaZulu-Natal, with subsequent local spread in the susceptible domestic dog population of southern Johannesburg. The vulnerability of the province was also highlighted through multiple, dead-end introductions in the past ten years. This is the first report of a rabies outbreak in the greater Johannesburg area with evidence of local transmission in the domestic dog population.

Background: Since 1995, measles vaccination at nine and 18 months has been routine in South Africa; however, coverage seldom reached >95%. We describe the epidemiology of laboratory-confirmed measles case-patients and assess the impact of the nationwide mass vaccination campaign during the 2009 to 2011 measles outbreak in South Africa., Methods: Serum specimens collected from patients with suspected-measles were tested for measles-specific IgM antibodies using an enzyme-linked immunosorbent assay and genotypes of a subset were determined. To estimate the impact of the nationwide mass vaccination campaign, we compared incidence in the seven months pre- (1 September 2009-11 April 2010) and seven months post-vaccination campaign (24 May 2010-31 December 2010) periods in seven provinces of South Africa., Results: A total of 18,431 laboratory-confirmed measles case-patients were reported from all nine provinces of South Africa (cumulative incidence 37 per 100,000 population). The highest cumulative incidence per 100,000 population was in children aged <1 year (603), distributed as follows: <6 months (302/100,000), 6 to 8 months (1083/100,000) and 9 to 11 months (724/100,000). Forty eight percent of case-patients were ≥ 5 years (cumulative incidence 54/100,000). Cumulative incidence decreased with increasing age to 2/100,000 in persons ≥ 40 years. A single strain of measles virus (genotype B3) circulated throughout the outbreak. Prior to the vaccination campaign, cumulative incidence in the targeted vs. non-targeted age group was 5.9-fold higher, decreasing to 1.7 fold following the campaign (P<0.001) and an estimated 1,380 laboratory-confirmed measles case-patients were prevented., Conclusion: We observed a reduction in measles incidence following the nationwide mass vaccination campaign even though it was conducted approximately one year after the outbreak started. A booster dose at school entry may be of value given the high incidence in persons >5 years.

Rabies remains a global public health problem but increasingly so in the developing world. Given a lack of awareness, priority and diagnostic capability, very few developing countries, especially in Africa, report on laboratory confirmed human rabies cases. Here we present a retrospective study on the epidemiology of human rabies in Republic of South Africa for a 25-year period, 1983-2007, based on laboratory confirmed cases. The study highlights the role of the domestic dog as a reservoir and vector of rabies and contrasts this to the almost negligible contribution of wildlife vectors to the overall burden of human rabies in dog rabies endemic areas. From the collective data set, epidemiological aspects that include various features of these human rabies cases as well as failures in or towards the treatment of exposures are reported. Molecular analysis of virus isolates did not identify any additional cases of rabies attributed to infection with the Duvenhage, Lagos bat or Mokola or any other rabies-related viruses., (Copyright © 2010 Elsevier B.V. All rights reserved.)

The A.J. Orenstein Memorial Lecture, Medical School, Univ. of the Witwatersrand, Johannesburg, 12 August 2009

Duvenhage virus was isolated from a patient who died of a rabies-like disease after being scratched by a bat early in 2006. This occurred approximately 80 km from the site where the only other known human infection with the virus had occurred 36 years earlier.

In a 3,000-bed tertiary care hospital, 88 cases of methicillin-resistant Staphylococcus aureus (MRSA) bacteraemia were identified from 22,383 blood cultures (0.39%) submitted to the microbiology laboratory over a one-year period. Two high-risk areas were identified: the paediatric oncology unit, in which 12 cases of MRSA bacteraemia were identified from 924 blood cultures (1.3%), and the intensive care unit (ICU), in which 14 cases of MRSA bacteraemia were identified from 1,391 blood cultures (1.0%). In a one-year targeted intervention programme in which staff and patients were screened for MRSA carriage, patient carriers isolated, and mupirocin and chlorhexidine treatment administered, the number of MRSA bacteraemia cases decreased in these areas to 0 and 4, respectively (p = 0.000123 and 0.016), while the incidence of MRSA bacteraemia in non-targeted areas increased from 62 of 20,068 blood cultures (0.3%) to 82 of 18,784 blood cultures (0.44%) (p = 0.047). In the year post intervention the incidence of MRSA bacteraemia increased to 3 of 815 cultures (0.37%) in the paediatric oncology unit, 10 of 1,934 cultures (0.5%) in the ICU, and 112 of 18,977 cultures (0.59%) in the rest of the hospital (p = 0.00004 versus preintervention period). This study demonstrates the efficacy of targeted MRSA control measures in a hospital in which MRSA is endemic.