Remembering Professor Peter A. Leggat, AM, ADC (1961-2023)

Professor Peter Leggat, the Immediate Past President of the Australasian College of Tropical Medicine (ACTM), passed away peacefully in Brisbane on 20 September 2023 [...].

Brucellosis Seropositivity Using Three Serological Tests and Associated Risk Factors in Abattoir Workers in Gauteng Province, South Africa

Abattoir workers are liable to zoonotic infections from animals and animal products, primarily to diseases with asymptomatic and chronic clinical manifestations in animals, such as brucellosis. No published reports exist on the seroprevalence of brucellosis in abattoir workers in South Africa. Therefore, this cross-sectional study was conducted to estimate the occurrence and risk factors for Brucella exposure in abattoir workers in Gauteng Province. A total of 103 abattoir workers and managers from 6 abattoirs, where brucellosis-positive slaughtered cattle and sheep were previously detected, were interviewed and tested with serological assays using the Rose Bengal test (RBT), BrucellaCapt, and IgG-ELISA. A pre-tested questionnaire was administered to consenting respondents to obtain information on risk factors for brucellosis. Of the 103 respondents tested, the distribution of female and male workers was 16 (15.5%) and 87 (84.5%), respectively. The seroprevalence for exposure to brucellosis was 21/103 (20.4%, 95%CI: 13.1-29.5) using a combination of RBT, BrucellaCapt, or IgG-ELISA. For test-specific results, seroprevalences by RBT, BrucellaCapt, and IgG-ELISA were 13/103 (12.6%, 95%CI: 6.9-20.6), 9/103 (8.74%, 95%CI: 4.1-15.9), and 18/103 (17.5%, 95%CI: 10.7-26.2), respectively. Low-throughput abattoirs were identified as associated risks, as 29.3% of workers were seropositive compared with 12.7% of workers in high-throughput abattoirs, which highlights that direct contact at abattoirs poses higher risk to workers than indirect and direct contact outside abattoirs. This study confirms the occurrence of Brucella spp. antibodies among abattoir workers in South Africa, possibly due to occupational exposure to Brucella spp., and highlights the occupational hazard to workers. Furthermore, findings underscore that abattoir facilities can serve as points for active and passive surveillance for indicators of diseases of public health importance. We recommend periodic implementation of brucellosis testing of abattoir workers country-wide to establish baseline data for informing appropriate preventive practices and reducing the potential burden of infection rates among these high-risk workers.

Forgotten but not gone in rural South Africa: Urinary schistosomiasis and implications for chronic kidney disease screening in endemic countries

Background: Urinary schistosomiasis caused by infection with Schistosoma haematobium ( S. haematobium) remains endemic in Africa and is associated with haematuria and albuminuria/proteinuria. Kidney Disease Improving Global Outcomes clinical guidelines recommend evaluating proteinuria/albuminuria and glomerular filtration rate for chronic kidney disease (CKD) diagnosis. The guidelines are informed by population data outside of Africa but have been adopted in many African countries with little validation. Our study aimed to characterise the burden of urinary schistosomiasis in rural South Africa (SA) and evaluate its relationship with markers of kidney dysfunction with implications for CKD screening. Methods: In this population-based cohort study, we recruited 2021 adults aged 20 - 79 years in the Mpumalanga Province, SA. Sociodemographic data were recorded, urinalysis performed, and serum creatinine and urine albumin and creatinine measured. Kidney dysfunction was defined as an estimated glomerular filtration rate (eGFR) <60ml/min/1.73m 2 and/or urine albumin-creatinine ratio >3.0mg/mmol. S . haematobium infection was determined by urine microscopy. Multivariable analyses were performed to determine relationships between S. haematobium and markers of kidney dysfunction. Results: Data were available for 1226 of 2021 participants. 717 (58.5%) were female and the median age was 35 years (IQR 27 - 47). Prevalence of kidney dysfunction and S. haematobium was 20.2% and 5.1% respectively. S. haematobium was strongly associated with kidney dysfunction (OR 8.66; 95% CI 4.10 - 18.3) and related to albuminuria alone (OR 8.69; 95% CI 4.11 - 18.8), with no evidence of an association with eGFR <90ml/min/1.73m 2 (OR 0.43; 95% CI 0.05 - 3.59). Discussion: The strong association between urinary schistosomiasis and albuminuria requires careful consideration when screening for CKD. Screening for, and treatment of, schistosomiasis should be a routine part of initial work-up for CKD in S. haematobium endemic areas. Urinary schistosomiasis, a neglected tropical disease, remains a public health concern in the Mpumulanga province of SA.

Forgotten but not gone in rural South Africa: Urinary schistosomiasis and implications for chronic kidney disease screening in endemic countries

Background: Urinary schistosomiasis caused by infection with Schistosoma haematobium ( S. haematobium) remains endemic in Africa and is associated with haematuria and albuminuria/proteinuria. Kidney Disease Improving Global Outcomes clinical guidelines recommend evaluating proteinuria/albuminuria and glomerular filtration rate for chronic kidney disease (CKD) diagnosis. The guidelines are informed by population data outside of Africa but have been adopted in many African countries with little validation. Our study aimed to characterise the burden of urinary schistosomiasis in rural South Africa (SA) and evaluate its relationship with markers of kidney dysfunction with implications for CKD screening. Methods: In this population-based cohort study, we recruited 2021 adults aged 20 - 79 years in the Mpumalanga Province, SA. Sociodemographic data were recorded, urinalysis performed, and serum creatinine and urine albumin and creatinine measured. Kidney dysfunction was defined as an estimated glomerular filtration rate (eGFR) <60ml/min/1.73m 2 and/or urine albumin-creatinine ratio >3.0mg/mmol. S . haematobium infection was determined by urine microscopy. Multivariable analyses were performed to determine relationships between S. haematobium and markers of kidney dysfunction. Results: Data were available for 1226 of 2021 participants. 717 (58.5%) were female and the median age was 35 years (IQR 27 - 47). Prevalence of kidney dysfunction and S. haematobium was 20.2% and 5.1% respectively. S. haematobium was strongly associated with kidney dysfunction (OR 8.66; 95% CI 4.10 - 18.3) and related to albuminuria alone (OR 8.69; 95% CI 4.11 - 18.8), with no evidence of an association with eGFR <90ml/min/1.73m 2 (OR 0.43; 95% CI 0.05 - 3.59). Discussion: The strong association between urinary schistosomiasis and albuminuria requires careful consideration when screening for CKD. Screening for, and treatment of, schistosomiasis should be a routine part of initial work-up for CKD in S. haematobium endemic areas. Urinary schistosomiasis, a neglected tropical disease, remains a public health concern in the Mpumulanga province of SA.

Neoehrlichiosis in Symptomatic Immunocompetent Child, South Africa

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.

COVID-19: Current Status and Future Prospects

This second Special Issue in a series of Special Issues in Tropical Medicine and Infectious Disease looks at recent global research on the current Coronavirus (COVID-19) Pandemic [...].

Trends in the prevalence of microscopically-confirmed schistosomiasis in the South African public health sector, 2011-2018

Background

Schistosomiasis, also known as bilharzia, is a chronic parasitic blood fluke infection acquired through contact with contaminated surface water. The illness may be mild or can cause significant morbidity with potentially serious complications. Children and those living in rural areas with limited access to piped water and services for healthcare are the most commonly infected. To address the prevalence of the disease in parts of South Africa (SA) effective national control measures are planned, but have not yet been implemented. This study aimed to estimate the prevalence and trends of public sector laboratory-confirmed schistosomiasis cases in SA over an eight-year (2011–2018) period, to inform future control measures.

Methodology & principal findings

This is a descriptive analysis of secondary data from the National Health Laboratory Service (NHLS). The study included all records of patients for whom microscopic examination detected Schistosoma species eggs in urine or stool specimens from January 2011 to December 2018. Crude estimates of the prevalence were calculated using national census mid-year provincial population estimates as denominators, and simple linear regression was used to analyse prevalence trends. A test rate ratio was developed to describe variations in testing volumes among different groups and to adjust prevalence estimates for testing variations.

A total number of 135 627 schistosomiasis cases was analysed with the highest prevalence observed among males and individuals aged 5–19 years. We describe ongoing endemicity in the Eastern Cape Province, and indicate important differences in the testing between population groups.

Conclusion

While there was no overall change in the prevalence of schistosomiasis during the analysis period, an average of 36 people per 100 000 was infected annually. As such, this represents an opportunity to control the disease and improve quality of life of affected people. Laboratory-based surveillance is a useful method for reporting occurrence and evaluating future intervention programs where resources to implement active surveillance are limited.

This is the first paper to describe the prevalence of human schistosomiasis in South Africa using nationally representative data. The prevalence remained consistent during the eight-year period, independent of increasing annual testing volumes. Groups with the highest burden included males and individuals aged 5–19 years. The schistosomiasis-endemic provinces of Limpopo, Mpumalanga and KwaZulu-Natal emerged as the highest-burdened areas, and ongoing endemicity in Eastern Cape Province was demonstrated. Western Cape Province likely reported cases imported from endemic provinces rather than being acquired by local transmission. In summary, schistosomiasis remains an important public health problem in South Africa that needs long-term sustainable, effective standardised interventions to reduce the burden. Passive laboratory-based surveillance is a practical tool for reporting prevalence, and could be used to monitor and evaluate future intervention programs.

Improving the quality of malaria diagnosis in southern Africa through the development of a regional malaria slide bank

Background

A malaria slide bank (MSB) is a useful asset for any malaria microscopy testing laboratory to have access to. However, it is not feasible for every country to have its own MSB. If countries are able to pool their resources, a regional MSB is a viable solution. This paper describes the methodology, costing and lessons learnt of establishing and maintaining an MSB over a 3-year period, for a Southern Africa Development Community region.

Methods

A national reference laboratory in South Africa was granted funding for setting up the MSB; it possessed experienced staff and suitable resources. Two additional full-time personnel were employed to carry out the activities of this project. Strict protocols for donor/patient blood sample screening, smear preparation, mass staining, quality control and slide validation were followed. Slides from the MSB were used for training and proficiency testing purposes. The initial and recurrent yearly costs to set up and maintain the MSB were calculated.

Results

Over 35 months, 154 batches (26,623 slides) were prepared; the majority were Plasmodium falciparum. Ninety-two percent (141/154) of batches passed internal quality control, and 89% (93/104) passed external validation. From these slides, two training slide sets and six proficiency testing slide sets were sent out. The initial year’s cost to establish an MSB was calculated at approximately $165,000, and the recurrent year-on-year cost was $130,000.

Conclusions

The key components for maintaining a high-quality MSB are consistent funding, competent staff and adherence to standardized protocols. Travel to malaria-endemic areas for access to non-falciparum malaria species, and dilution of P. falciparum blood to desired parasite densities, are extremely useful to ensure variety. The MSB created here supported multiple laboratories in eight countries, and has the potential to expand.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12936-021-03899-5.

Anthemosoma garnhami in an HIV-Infected Man from Zimbabwe Living in South Africa

An HIV-positive man from Zimbabwe living in South Africa sought treatment for multiple clinical signs, including fever, weight loss, anemia, and splenomegaly. We identified in his blood an African rodent piroplasm, Anthemosoma garnhami, related to Babesia species. This finding extends the known geographic and host range of A. garnhami.

Fatal Rodentborne Leptospirosis in Prison Inmates, South Africa, 2015

Leptospirosis is a neglected zoonotic disease. In 2015, leptospirosis was diagnosed in 2 prison inmates in South Africa. Using real-time PCR and DNA sequencing, we identified Leptospira interrogans serogroup Icterohaemorrhagiae in rodents and water samples within the prison. Leptospirosis might be frequently underdiagnosed in South Africa.

Anaplasma phagocytophilum and Other Anaplasma spp. in Various Hosts in the Mnisi Community, Mpumalanga Province, South Africa

DNA samples from 74 patients with non-malarial acute febrile illness (AFI), 282 rodents, 100 cattle, 56 dogs and 160 Rhipicephalus sanguineus ticks were screened for the presence of Anaplasma phagocytophilum DNA using a quantitative PCR (qPCR) assay targeting the msp2 gene. The test detected both A. phagocytophilum and Anaplasma sp. SA/ZAM dog DNA. Microbiome sequencing confirmed the presence of low levels of A. phagocytophilum DNA in the blood of rodents, dogs and cattle, while high levels of A. platys and Anaplasma sp. SA/ZAM dog were detected in dogs. Directed sequencing of the 16S rRNA and gltA genes in selected samples revealed the presence of A. phagocytophilum DNA in humans, dogs and rodents and highlighted its importance as a possible contributing cause of AFI in South Africa. A number of recently described Anaplasma species and A. platys were also detected in the study. Phylogenetic analyses grouped Anaplasma sp. SA/ZAM dog into a distinct clade, with sufficient divergence from other Anaplasma species to warrant classification as a separate species. Until appropriate type-material can be deposited and the species is formally described, we will refer to this novel organism as Anaplasma sp. SA dog.

Multi-locus sequence analyses reveal a clonal L. borgpetersenii genotype in a heterogeneous invasive Rattus spp. community across the City of Johannesburg, South Africa

BACKGROUND

Rattus spp. are frequently implicated as key reservoir hosts for leptospirosis, one of the most common, but neglected, bacterial zoonoses in the world. Although leptospirosis is predicted to be a significant public health threat in Africa, studies from the continent are limited.

METHODS

Rattus spp. (n = 171) were sampled (January-May 2016) across the City of Johannesburg, South Africa's largest inland metropole. Rattus spp. genetic diversity was evaluated by full length (1140 bp) cyt b sequencing of 42 samples. For comparison, a further 12 Rattus norvegicus samples collected in Cape Town, South Africa's largest coastal metropole, were also genotyped. Leptospira infections were identified and genotyped using real-time PCR and multi-locus (lfb1, secY and lipL41) DNA sequencing.

RESULTS

Five R. norvegicus haplotypes were identified across Johannesburg, four of which have not previously been detected in South Africa, and one in Cape Town. Across Johannesburg we identified a Leptospira spp. infection prevalence of 44% (75/171) and noted significant differences in the prevalence between administrative regions within the metropole. Multi-locus sequence analyses identified a clonal genotype consistent with L. borgpetersenii serogroup Javanica (serovar Ceylonica).

DISCUSSION

The prevalence of infection identified in this study is amongst the highest detected in Rattus spp. in similar contexts across Africa. Despite the complex invasion history suggested by the heterogeneity in R. norvegicus haplotypes identified in Johannesburg, a single L. borgpetersenii genotype was identified in all infected rodents. The lack of L. interrogans in a rodent community dominated by R. norvegicus is notable, given the widely recognised host-pathogen association between these species and evidence for L. interrogans infection in R. norvegicus in Cape Town. It is likely that environmental conditions (cold, dry winters) in Johannesburg may limit the transmission of L. interrogans. Spatial heterogeneity in prevalence suggest that local factors, such as land use, influence disease risk in the metropole.

CONCLUSIONS

In South Africa, as in other African countries, leptospirosis is likely underdiagnosed. The high prevalence of infection in urban rodents in Johannesburg suggest that further work is urgently needed to understand the potential public health risk posed by this neglected zoonotic pathogen.

Implementing malaria control in South Africa, Eswatini and southern Mozambique during the COVID-19 pandemic

The COVID-19 pandemic has strained healthcare delivery systems in a number of southern African countries. Despite this, it is imperative that malaria control and elimination activities continue, especially to reduce as far as possible the number and rate of hospitalisations caused by malaria. The implementation of enhanced malaria control/elimination activities in the context of COVID-19 requires measures to protect healthcare workers and the communities they serve. The aim of this review is therefore to present innovative ideas for the timely implementation of malaria control without increasing the risk of COVID-19 to healthcare workers and communities. Specific recommendations for parasite and vector surveillance, diagnosis, case management, mosquito vector control and community outreach and sensitisation are given.

Gnathostomiasis Acquired by Visitors to the Okavango Delta, Botswana

Gnathostomiasis is a zoonotic nematode parasite disease, most commonly acquired by eating raw or undercooked fish. Although the disease is well known in parts of Asia and Central and South America, relatively few cases have been reported from Africa. Raw fish consumed in the Okavango River delta area of Botswana, and in nearby western Zambia, has previously produced laboratory-proven gnathostomiasis in tourists. The purpose of this communication is to record additional cases of the infection acquired in the Okavango delta, and to alert visitors to the inadvisability of eating raw freshwater fish in the southern African region.

External Quality Assessment of Bacterial Identification and Antimicrobial Susceptibility Testing in African National Public Health Laboratories, 2011-2016

Background: In 2002, the World Health Organization (WHO) launched a regional microbiology external quality assessment (EQA) programme for national public health laboratories in the African region, initially targeting priority epidemic-prone bacterial diseases, and later including other common bacterial pathogens. Objectives: The aim of this study was to analyse the efficacy of an EQA programme as a laboratory quality system evaluation tool. Methods: We analysed the proficiency of laboratories’ performance of bacterial identification and antimicrobial susceptibility testing (AST) for the period 2011–2016. The National Institute for Communicable Diseases of South Africa provided technical coordination following an agreement with WHO, and supplied EQA samples of selected bacterial organisms for microscopy (Gram stain), identification, and antimicrobial susceptibility testing (AST). National public health laboratories, as well as laboratories involved in the Invasive Bacterial Diseases Surveillance Network, were enrolled by the WHO Regional Office for Africa to participate in the EQA programme. We analysed participants’ results of 41 surveys, which included the following organisms sent as challenges: Streptococcus pneumonia, Haemophilus influenzae, Neisseria meningitidis, Salmonella Typhi, Salmonella Enteritidis, Shigella flexneri, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus anginosus, Enterococcus faecium, Serratia marcescens, Acinetobacter baumannii, and Enterobacter cloacae. Results: Eighty-one laboratories from 45 countries participated. Overall, 76% of participants obtained acceptable scores for identification, but a substantial proportion of AST scores were not in the acceptable range. Of 663 assessed AST responses, only 42% had acceptable scores. Conclusion: In the African Region, implementation of diagnostic stewardship in clinical bacteriology is generally suboptimal. This report illustrates that AST is poorly done compared to microscopy and identification. It is critically important to make the case for implementation of quality assurance in AST, as it is the cornerstone of antimicrobial resistance surveillance reporting and implementation of the Global Antimicrobial Resistance Surveillance System.

Absence of kelch13 artemisinin resistance markers but strong selection for lumefantrine-tolerance molecular markers following 18 years of artemisinin-based combination therapy use in Mpumalanga Province, South Africa (2001-2018)

Background

The ability of Plasmodium falciparum parasites to develop resistance to widely used anti-malarials threatens malaria control and elimination efforts. Regular drug efficacy monitoring is essential for ensuring effective treatment policies. In low transmission settings where therapeutic efficacy studies are often not feasible, routine surveillance for molecular markers associated with anti-malarial resistance provides an alternative for the early detection of emerging resistance. Such a longitudinal survey of changes in the prevalence of selected molecular markers of resistance was conducted in the malaria-endemic regions of Mpumalanga Province, South Africa, where malaria elimination at a district-level is being pursued.

Methods

Molecular analyses to determine the prevalence of alleles associated with resistance to lumefantrine (mdr86N, crt76K and mdr1 copy number variation) and sulfadoxine–pyrimethamine (dhfr triple, dhps double, SP quintuple) were conducted between 2001 and 2018, while artemisinin resistance markers (kelch13 mutations) were assessed only in 2018.

Results

Parasite DNA was successfully amplified from 1667/2393 (70%) of malaria-positive rapid diagnostic tests routinely collected at primary health care facilities. No artemisinin resistance-associated kelch13 mutations nor amplification of the mdr1 gene copy number associated with lumefantrine resistance were observed. However, prevalence of both the mdr86N and crt76K alleles increased markedly over the study period, with all isolates collected in 2018 carrying these markers. SP quintuple mutation prevalence increased steadily from 14% in 2001 to 96% in 2018. Mixed alleles at any of the codons assessed were rare by 2018.

Conclusion

No kelch13 mutations confirmed or suspected to be associated with artemisinin resistance were identified in 2018. Although parasites carrying the mdr86N and crt76K alleles associated with reduced lumefantrine susceptibility were strongly selected for over the study period, nearing fixation by 2018, the marker for lumefantrine resistance, namely increased mdr1 copy number, was not observed in this study. The increase in mdr86N and crt76K allele prevalence together with intense regional artemether–lumefantrine drug pressure, raises concern regarding the sustained artemether–lumefantrine efficacy. Regular, rigorous anti-malarial resistance marker surveillance across all three South African malaria-endemic provinces to inform case management is recommended.

South African Tick Bite Fever: An Overview

The rickettsiae are a diverse group of vector-borne zoonotic bacterial pathogens. The two common spotted fever diseases in existence in southern Africa are boutonneuse fever-like tick bite fever (TBF), caused by Rickettsia conorii, and African TBF, caused by R. africae. This review addresses demographic, epidemiological, clinical, diagnostic, therapeutic, and preventive aspects of TBF in the southern African context, including a discussion of the dermatopathological findings and potential diagnostic pitfalls.

Safety and tolerability of single low-dose primaquine in a low-intensity transmission area in South Africa: an open-label, randomized controlled trial

Background

To reduce onward falciparum malaria transmission, the World Health Organization recommends adding single low-dose (SLD) primaquine to artemisinin-based combination treatment in low transmission areas. However, uptake of this recommendation has been relatively slow given concerns about whether individual risks justify potential community benefit. This study was undertaken to generate comprehensive local data on the risk–benefit profile of SLD primaquine deployment in a pre-elimination area in South Africa.

Methods

This randomized, controlled open-label trial investigated adding a single low primaquine dose on day 3 to standard artemether–lumefantrine treatment for uncomplicated falciparum malaria. Efficacy, safety and tolerability of artemether–lumefantrine and primaquine treatment were assessed on days 3, 7, 14, 28 and 42. Lumefantrine concentrations were assayed from dried blood spot samples collected on day 7.

Results

Of 217 patients screened, 166 were enrolled with 140 randomized on day 3, 70 to each study arm (primaquine and no primaquine). No gametocytes were detected by either microscopy or PCR in any of the follow-up samples collected after randomization on day 3, precluding assessment of primaquine efficacy. Prevalence of the CYP2D6*4, CYP2D6*10 and CYP2D6*17 mutant alleles was low with allelic frequencies of 0.02, 0.11 and 0.16, respectively; none had the CYP2D6*4/*4 variant associated with null activity. Among 172 RDT-positive patients G6PD-genotyped, 24 (14%) carried the G6PD deficient (A−) variant. Median haemoglobin concentrations were similar between treatment arms throughout follow-up. A third of participants had a haemoglobin drop > 2 g/dL; this was not associated with primaquine treatment but may be associated with G6PD genotype [52.9% (9/17) with A− genotype vs. 31% (36/116) with other genotypes (p = 0.075)]. Day 7 lumefantrine concentrations and the number and nature of adverse events were similar between study arms; only one serious adverse event occurred (renal impairment in the no primaquine arm). The artemether–lumefantrine PCR-corrected adequate clinical and parasitological response rate was 100%, with only one re-infection found among the 128 patients who completed 42-day follow-up.

Conclusions

Safety, tolerability, CYP2D6 and G6PD variant data from this study support the deployment of the WHO-recommended SLD primaquine without G6PD testing to advance malaria elimination in South African districts with low-intensity residual transmission.

Trial registration Pan African Clinical Trial Registry, PACTR201611001859416. Registered 11 November 2016, https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=1859

Risk factors for bacterial zoonotic pathogens in acutely febrile patients in Mpumalanga Province, South Africa

Endemic zoonoses, such as Q fever and spotted fever group (SFG) rickettsiosis, are prevalent in South Africa, yet often undiagnosed. In this study, we reviewed the demographics and animal exposure history of patients presenting with acute febrile illness to community health clinics in Mpumalanga Province to identify trends and risk factors associated with exposure to Coxiella burnetii, the causative agent of Q fever, and infection by SFG Rickettsia spp. Clinical and serological data and questionnaires elucidating exposure to animals and their products were obtained from 141 acutely febrile patients between 2012 and 2016. Exposure or infection status to C. burnetii and SFG Rickettsia spp. was determined by presence of IgG or IgM antibodies. Logistic regression models were built for risk factor analysis. Clinical presentation of patients infected by SFG rickettsiosis was described. There were 37/139 (27%) patients with a positive C. burnetii serology, indicative of Q fever exposure. Patients who had reported attending cattle inspection facilities ("dip tanks") were 9.39 times more likely to be exposed to Q fever (95% CI: 2.9-30.4). Exposure risk also increased with age (OR: 1.03, 95% CI: 1.002-1.06). Twenty-one per cent of febrile patients (24/118) had evidence of acute infection by SFG Rickettsia spp. Similarly, attending cattle inspection facilities was the most significant risk factor (OR: 8.48, 95% CI: 1.58-45.60). Seropositivity of females showed a significant OR of 8.0 when compared to males (95% CI: 1.49-43.0), and consumption of livestock was associated with a decreased risk (OR: 0.02, 95% CI: 0.001-0.54). A trend between domestic cat contact and SFG rickettsiosis was also noted, albeit borderline non-significant. In this endemic region of South Africa, an understanding of risk factors for zoonotic pathogens, including exposure to domestic animals, can help clinic staff with diagnosis and appropriate therapeutic management of acutely febrile patients as well as identify target areas for education and prevention strategies.

Clinical management of East African trypanosomiasis in South Africa: Lessons learned

BACKGROUND

East African trypanosomiasis is an uncommon, potentially lethal disease if not diagnosed and treated in a timely manner. South Africa, as a centre for emergency medical evacuations from much of sub-Saharan Africa, receives a high proportion of these patients, mostly tourists and expatriate residents.

METHODS

The cases of East African trypanosomiasis patients evacuated to South Africa, for whom diagnostic and clinical management advice was provided over the years 2004-2018, were reviewed, using the authors' own records and those of collaborating clinicians.

RESULTS

Twenty-one cases were identified. These originated in Zambia, Malawi, Zimbabwe, Tanzania, and Uganda. Nineteen cases (90%) had stage 1 (haemolymphatic) disease; one of these patients had fatal myocarditis. Of the two patients with stage 2 (meningoencephalitic) disease, one died of melarsoprol encephalopathy. Common problems were delayed diagnosis, erroneous assessment of severity, and limited access to treatment.

CONCLUSIONS

The key to early diagnosis is recognition of the triad of geographic exposure, tsetse fly bites, and trypanosomal chancre, plus good microscopy. Elements for successful management are rapid access to specific drug treatment, skilled intensive care, and good laboratory facilities. Clinical experience and the local stock of antitrypanosomal drugs from the World Health Organization have improved the chance of a successful outcome in the management of East African trypanosomiasis in South Africa; the survival rate over the period was 90.5%.

Prevalence of Selected Zoonotic Diseases and Risk Factors at a Human-Wildlife-Livestock Interface in Mpumalanga Province, South Africa

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.

Plague and listeriosis: current outbreaks, and an historical South African connection

No abdtract available.

Malaria reduces globally but rebounds across southern Africa

No abstract available.

Reviewing South Africa's malaria elimination strategy (2012-2018): progress, challenges and priorities

BACKGROUND

With a sustained national malaria incidence of fewer than one case per 1000 population at risk, in 2012 South Africa officially transitioned from controlling malaria to the ambitious goal of eliminating malaria within its borders by 2018. This review assesses the progress made in the 3 years since programme re-orientation while highlighting challenges and suggesting priorities for moving the malaria programme towards elimination.

METHODS

National malaria case data and annual spray coverage data from 2010 until 2014 were assessed for trends. Information on surveillance, monitoring and evaluation systems, human and infrastructure needs and community malaria knowledge was sourced from the national programme mid-term review.

RESULTS

Malaria cases increased markedly from 6811 in 2013 to 11,711 in 2014, with Mpumalanga and Limpopo provinces most affected. Enhanced local transmission appeared to drive malaria transmission in Limpopo Province, while imported malaria cases accounted for the majority of cases reported in Mpumalanga Province. Despite these increases only Vhembe and Mopani districts in Limpopo Province reported malaria incidences more than one case per 1000 population at risk by 2014. Over the review period annual spray coverage did not reach the recommended target of 90 % coverage, with information gaps identified in parasite prevalence, artemether-lumefantrine therapeutic utilization, asymptomatic/sub-patent carriage, drug efficacy, vector distribution and insecticide resistance.

CONCLUSIONS

Although South Africa has made steady progress since adopting an elimination agenda, a number of challenges have been identified. The heterogeneity of malaria transmission suggests interventions in Vhembe and Mopani districts should focus on control, while in KwaZulu-Natal Province eliminating transmission foci should be prioritized. Cross-border initiatives with neighbouring countries should be established/strengthened as a matter of urgency since malaria importation poses a real threat to the country's elimination efforts. It is also critical that provincial programmes are adequately resourced to effectively conduct the necessary targeted elimination activities, informed by current vector/parasite distribution and resistance data. More sensitive methods to detect sub-patent infections, primaquine as a transmission-blocking drug, and alternative vector control methods need to be investigated. Knowledge gaps among malaria health workers and affected communities should be identified and addressed.

Welcome to Tropical Medicine and Infectious Disease-A New Era in Open Access Publication

Historically, tropical medicine emerged from a multidisciplinary background as a result of progress in the areas of public health and hygiene, travel and exploration, biology and evolution, and the germ theory of disease [1].[...].

Cryptosporidium genotypes in children and calves living at the wildlife or livestock interface of the Kruger National Park, South Africa

Cryptosporidium infection is one of the most common causes of parasitic diarrhoea worldwide in cattle and humans. In developing countries, human cryptosporidiosis is most prevalent during early childhood and links between zoonotic infection and animal related activities have been demonstrated. This study investigated the prevalence and species/genotype distribution of Cryptosporidium among children (< 5 years) and calves (< 6 months) living in a rural farming area adjacent to the Kruger National Park in South Africa, where interactions between humans and wild and domestic animals are known to occur. Cryptosporidium oocysts were detected in 8/143 stool samples of children recruited within the hospital system (5.6%; 95% CI 2.4%, 10.7%) and in 2/352 faecal samples of calves (0.6%; 95% CI 0.1%, 2.0%) using the modified Ziehl–Neelsen (MZN) staining technique. Microscopy positive samples from children were further analysed by PCR targeting the 18S rRNA gene and identified as Cryptosporidium hominis (3/4) and Cryptosporidium meleagridis (1/4). Regardless of the microscopy outcome, randomly selected samples (n = 36) from calves 0–4 months of age were amplified and sequenced at the 18S rRNA gene using nested PCR. Two calves tested positive (5.6%; 95% CI 1.7%, 18.7%), and revealed the presence of Cryptosporidium parvum and Cryptosporidium bovis. The detection of only two zoonotic species (C. parvum in one calf and C. meleagridis in one child) suggests that zoonotic cryptosporidiosis is not currently widespread in our study area; however, the potential exists for amplification of transmission in an immunocompromised population.

Laboratory-based surveillance of Pneumocystis jirovecii pneumonia in South Africa, 2006–2010i

Background: We aimed to establish the characteristics of patients with confirmed Pneumocystis jirovecii pneumonia recruited by passive, sentinel laboratory-based surveillance.Method: The study design was prospective, observational, cross-sectional, laboratory-based sentinel surveillance. Laboratorybased surveillance of Pneumocystis jirovecii pneumonia (PJP), formerly known as Pneumocystis carinii pneumonia (PCP), was conducted in six South African provinces at 61 hospitals, of which 17 were sentinel sites, where surveillance officers collected clinical and demographic data from cases. A case was defined as a patient with a respiratory tract specimen that was confirmed positive for P. jirovecii by immunofluorescent microscopy or PCR test, either as a first diagnosis or ≥ 30 days after the last confirmed laboratory diagnosis of PJP. The chi-square test or Fisher’s exact test were used to compare the categorical variables.Results: From 2006–2010, 1 537 cases of PJP were recorded. Eighty-nine per cent (460/518) were found to be human immunodeficiency virus (HIV)-infected. This was a first diagnosis of HIV infection in 57% of the cases. The case fatality ratio was 34% (177/525). Recurrent infection was significantly more common in the 26- to 45-year age group, compared to children aged ≤ 5 years (odds ratio 1.7, 95% confidence interval: 1.1–2.8) (p 0.040). Treatment for tuberculosis was common in cases aged ≥ 5 years (37%, 85/229).Conclusion: PJP was the acquired immune deficiency syndrome-defining illness in more than half of the patients detected through laboratory-based surveillance. The high mortality rate and number of recurrent cases is noteworthy. This study may not have reflected the full spectrum of clinical presentation of the disease as case report forms were only completed for hospitalised patients at sentinel surveillance sites.

Anthrax as an example of the One Health concept

Anthrax is a peracute, acute or subacute multispecies bacterial infection that occurs on many continents. It is one of the oldest infectious diseases known; the biblical fifth and sixth plagues (Exodus chapters 7 to 9) that affected first livestock and then humans were probably anthrax. From the earliest historical records until development of an effective vaccine midway through the 20th Century, anthrax was one of the foremost causes of uncontrolled mortality in cattle, sheep, goats, horses and pigs, with 'spill over' into humans, worldwide. With the development of the Sterne spore vaccine, a sharp decline in anthrax outbreaks in livestock occurred during the 1930-1980 era. There were successful national vaccination programmes in many countries during this period, complemented by the liberal use of antibiotics and the implementation of quarantine regulations and carcass disposal. However, a resurgence of this disease in livestock has been reported recently in some regions, where complacency and a false sense of security have hindered vaccination programmes. The epidemiology of anthrax involves an environmental component, as well as livestock, wildlife and human components. This makes anthrax an ideal example for discussion in the One Health context. Many outbreaks of anthrax in wildlife are undetected or unreported, owing to surveillance inadequacies and difficulties. Human disease is generally acquired accidentally during outbreaks of anthrax in domestic livestock and wildlife. The exception is deliberate targeting of humans with anthrax in the course of biowarfare or bioterrorism.

Microsporidiosis in pediatric renal transplant patients in Cape Town, South Africa: two case reports

Microsporidia are an emerging group of pathogens associated with life-threatening opportunistic infections in immunocompromised hosts, particularly human immunodeficiency virus (HIV)-infected individuals. There have, however, been recent reports of infection in adult solid organ transplant recipients. We report two cases in children, to our knowledge the first in the paediatric literature. Two 13-yr-old, HIV-seronegative females received deceased donor renal transplants from the same donor. Both patients suffered acute cell-mediated rejection and CMV infection reactivation, managed with intensified immunosuppression and ganciclovir. Pyrexia of unknown origin and intermittent diarrhea in both prompted extensive investigations. In both patients, numerous spores of a microsporidial species were demonstrated in renal tissue on biopsy and in the urine, using modified trichrome and quick-hot Gram-chromotrope staining. Electron microscopy and PCR confirmed Encephalitozoon cuniculi infections. Both patients were successfully treated with 400 mg twice daily of albendazole, with sustained clinical improvement. We recommend that microsporidiosis be considered in the differential diagnosis of pyrexia of unknown origin in severely immunocompromised pediatric solid organ transplant recipients, particularly when associated with diarrhea.

Plasmodium ovale: a case of not-so-benign tertian malaria

Severe malaria is most commonly associated with Plasmodium falciparum. Plasmodium vivax is increasingly recognized as being capable of causing severe disease. In contrast, Plasmodium ovale is considered as a cause of benign disease and evidence supporting the occurrence of severe or complicated ovale infection is rare. This report describes a case of severe P. ovale infection in a patient presenting with jaundice, respiratory distress, severe thrombocytopenia, petechiae, and hypotension. He had no apparent underlying risk factors for severe disease.

Why did many more diamond miners than gold miners die in South Africa during the 1918 influenza pandemic?

The very large difference in mortality rates between Kimberley diamond miners and Witwatersrand gold miners during the 1918 influenza pandemic has never been explained. We examined extant epidemiological records from South African mining operations and other related activities to determine if mortality risk factors could be measured. During October 1918 when pandemic influenza struck in South Africa, the mortality rates in Kimberley diamond miners (22.4%, n = 11 445) were >35 times that of Rand gold miners (0.6%, n = 200 000). There were no differences discernable between diamond and gold miners regarding their recruitment, working conditions, housing or medical care that would explain the great variance in mortality rates. Reports of influenza-like illness in Natal Province some weeks prior to the main pandemic suggest infection from a mild version of influenza and thus protection of the gold miners from mortality whereas the more isolated diamond miners only experienced the second, more lethal, wave. The huge mortality difference between South African diamond and gold miners in 1918 is most likely explained by the circulation of a related but not identical virus to the A/H1N1 pandemic strain which reached Johannesburg prior to October 1918 because of its better transportation connections.

Crowdsourcing malaria parasite quantification: an online game for analyzing images of infected thick blood smears

Background

There are 600,000 new malaria cases daily worldwide. The gold standard for estimating the parasite burden and the corresponding severity of the disease consists in manually counting the number of parasites in blood smears through a microscope, a process that can take more than 20 minutes of an expert microscopist’s time.

Objective

This research tests the feasibility of a crowdsourced approach to malaria image analysis. In particular, we investigated whether anonymous volunteers with no prior experience would be able to count malaria parasites in digitized images of thick blood smears by playing a Web-based game.

Methods

The experimental system consisted of a Web-based game where online volunteers were tasked with detecting parasites in digitized blood sample images coupled with a decision algorithm that combined the analyses from several players to produce an improved collective detection outcome. Data were collected through the MalariaSpot website. Random images of thick blood films containing Plasmodium falciparum at medium to low parasitemias, acquired by conventional optical microscopy, were presented to players. In the game, players had to find and tag as many parasites as possible in 1 minute. In the event that players found all the parasites present in the image, they were presented with a new image. In order to combine the choices of different players into a single crowd decision, we implemented an image processing pipeline and a quorum algorithm that judged a parasite tagged when a group of players agreed on its position.

Results

Over 1 month, anonymous players from 95 countries played more than 12,000 games and generated a database of more than 270,000 clicks on the test images. Results revealed that combining 22 games from nonexpert players achieved a parasite counting accuracy higher than 99%. This performance could be obtained also by combining 13 games from players trained for 1 minute. Exhaustive computations measured the parasite counting accuracy for all players as a function of the number of games considered and the experience of the players. In addition, we propose a mathematical equation that accurately models the collective parasite counting performance.

Conclusions

This research validates the online gaming approach for crowdsourced counting of malaria parasites in images of thick blood films. The findings support the conclusion that nonexperts are able to rapidly learn how to identify the typical features of malaria parasites in digitized thick blood samples and that combining the analyses of several users provides similar parasite counting accuracy rates as those of expert microscopists. This experiment illustrates the potential of the crowdsourced gaming approach for performing routine malaria parasite quantification, and more generally for solving biomedical image analysis problems, with future potential for telediagnosis related to global health challenges.

Leptospirosis in South Africa

Leptospirosis is a common zoonosis worldwide. It has a ubiquitous distribution and causes a wide spectrum of disease. Leptospirosis therefore has a broad reservoir host range, and many infected species of animals excrete leptospires in their urine, which leads to contamination of soil and water. Typical descriptions of the disease include a biphasic (anicteric form) and fulminant disease in the icterohaemorrhagic form. Only a few local case reports of human leptospirosis have been published, the most recent one being in 1974. A rodent-related zoonosis study (RatZooMan) was conducted from 2003 until 2006 in three provinces (Limpopo, KwaZulu-Natal and the Eastern Cape). Of the people sampled in Cato Crest (Durban, KwaZulu-Natal Province), 43/217 (19.8%) were seropositive for leptospirosis. Of the clinical samples sent to the Special Bacterial Pathogens Reference Unit from all over the country for testing in 2009, 16/176 (9%) were IgM positive; in 2010 and January 2011 to May 2011, 14/215 (6.5%) and 12/96 (12.5%), respectively, were IgM positive.The apparent incidence of leptospirosis in the South African population is moderately high based on the detected positives in suspected cases; it is thought that the circulating infection rate may be even higher when looking at the RatZooMan results. This may be due to underreporting and undiagnosed cases. Communities in informal settlements in urban areas are especially at risk as infected rodent populations are a continuous source of transmission.

Human cystic echinococcosis in South Africa

Cystic echinococcosis (CE) is caused by the tapeworm, Echinococcus granulosus. The tapeworms resides in the small intestines of canids and the lifecycle involves both intermediate and definitive hosts. Humans are accidental intermediate hosts. Cystic echinococcosis is an economically important infection constituting a threat to public health, and is considered an emerging disease around the world. There are at least 10 Echinococcus strain types (G1 – G10), each exhibiting diversity of morphology, development and host range. The epidemiology of CE is poorly understood in South Africa. A retrospective data analysis of the National Health Laboratory Service (NHLS) laboratory information system on echinococcosis serology, microscopy and histopathology results in eight provinces (excluding KwaZula-Natal) showed an overall positivity rate in submitted diagnostic samples of 17.0% (1056/6211), with the Eastern Cape (30.4%), North West (19.0%) and Northern Cape (18.0%) provinces showing highest rates. The data showed considerable variability between provinces. The review also showed that most proven cases were negative on serology, implying that the actual number of patients could be underestimated. To our knowledge, no data exist about the prevalent strains of E. granulosus and this prospective study will attempt to fill that gap. The aim is to genotype strains causing the disease in South Africa. Two different polymerase chain reaction (PCR) methods will be used to respectively target the 12S rRNA and nad 1 genes. To date, three samples have been genotyped as G1, G5 and G6; suggesting diversity of strains prevalent in the country, but more data is needed for a clearer picture.

<i>Bartonella henselae</i> and <i>Bartonella quintana</i> seroprevalence in HIV-positive, HIV-negative and clinically healthy volunteers in Gauteng, South Africa

Bartonella is a genus of opportunistic, Gram-negative bacilli transmitted from animals to human hosts. Bartonellae are newly emerging pathogens that can cause a variety of clinical manifestations in both immunocompromised and healthy persons.The aims were to determine the IgG and IgM seroprevalences of Bartonella henselae and Bartonella quintana in immunocompromised and immunocompetent individuals using an immunofluorescence assay (IFA).A total of 382 HIV-positive outpatients of the Chris Hani Baragwanth HIV-clinic, 382 retrospective residual samples from HIV-negative antenatal patients, and 42 clinically healthy volunteers were tested using a commercially available IFA kit to determine the prevalence of IgG and IgM antibodies to B. henselae and B. quintana.The IgM and IgG seroprevalences for the HIV-positive patients were 14% (53/382) and 32% (121/382), respectively, compared to 18% for both IgM (62/342) and IgG (63/342) in the HIV- negative antenatal patients. Similarly, the prevalence for IgM was 17% (7/42) and IgG was 19% (8/42) for the clinically healthy volunteers.HIV-positivity appears to be a significant risk factor for Bartonella infection, compared with healthy subjects. Although IFAs have a high sensitivity for Bartonella antibody detection, they have various limitations including cross-reactivity with other closely-related human pathogens.

Unexpectedly low seroprevalence of toxoplasmosis in South Africa

Toxoplasmosis is an infection of warm-blooded vertebrates caused by the obligate intracellular protozoan parasite, Toxoplasma gondii. It is one of the most common parasitic diseases of humans, infecting approximately one-third of the world’s population. In persons with advanced HIV, toxoplasmosis represents a major opportunistic infection of the central nervous system. Approximately two-thirds of all people living with HIV live in sub-Saharan Africa. In areas such as this, toxoplasmosis could theoretically pose a huge threat. There is little known about T. gondii prevalence in humans in Africa. Geographically, prevalences vary widely on this continent, as observed in other parts of the world. There is limited historical information about the disease in South Africa. More knowledge is needed at a regional level about the risk of toxoplasmosis, diagnostic issues, and measures to reduce the risk to susceptible persons. The seroprevalence of T. gondii in selected populations, namely HIV-positive and HIV-negative individuals, and a more general sample biased towards pregnant women, was therefore investigated and found to be 9.8% (37/376), 12.8% (48/376) and 6.4% (32/497) respectively. Compared with historical data from South Africa, the prevalence has decreased substantially; however, the incidence of clinical disease is unknown, despite the very high burden of HIV and AIDS cases (5.9 million and 0.7 million, respectively in 2009). This study provided information relating to the diagnosis and current seroprevalence of T. gondii in South Africa. Many questions still remain to be answered however, to fully understand the impact of this parasite on the country’s population.