BackgroundIn August 2014, the National Institute for Communicable Diseases (NICD) in South Africa established a modular high-biosafety field Ebola diagnostic laboratory (SA FEDL) near Freetown, Sierra Leone in response to the rapidly increasing number of Ebola virus disease (EVD) cases.Methods and findingsThe SA FEDL operated in the Western Area of Sierra Leone, which remained a “hotspot” of the EVD epidemic for months. The FEDL was the only diagnostic capacity available to respond to the overwhelming demand for rapid EVD laboratory diagnosis for several weeks in the initial stages of the EVD crisis in the capital of Sierra Leone. Furthermore, the NICD set out to establish local capacity amongst Sierra Leonean nationals in all aspects of the FEDL functions from the outset. This led to the successful hand-over of the FEDL to the Sierra Leone Ministry of Health and Sanitation in March 2015. Between 25 August 2014 and 22 June 2016, the laboratory tested 11,250 specimens mostly from the Western Urban and Western Rural regions of Sierra Leone, of which 2,379 (21.14%) tested positive for Ebola virus RNA.ConclusionsThe bio-safety standards and the portability of the SA FEDL, offered a cost-effective and practical alternative for the rapid deployment of a field-operated high biocontainment facility. The SA FEDL teams demonstrated that it is highly beneficial to train the national staff in the course of formidable disease outbreak and accomplished their full integration into all operational and diagnostic aspects of the laboratory. This initiative contributed to the international efforts in bringing the EVD outbreak under control in Sierra Leone, as well as capacitating local African scientists and technologists to respond to diagnostic needs that might be required in future outbreaks of highly contagious pathogens.

Summary The diversity of Cryptosporidium at species, subtype family and subtype level in diarrhoeic children was investigated in four provinces in South Africa. A total of 442 stool samples from children <5 years of age were collected under a large rotavirus surveillance programme and analysed by Ziehl–Neelsen acid‐fast staining. Fifty‐four (12.2%) were positive for Cryptosporidium, of which 25 were genotyped by polymerase chain reaction (PCR)–restriction fragment length polymorphism (RFLP) and DNA sequence analyses of the 18S rRNA gene. The majority of genotyped specimens were identified as C. hominis (76%), and a high genetic diversity was found with five different C. hominis subtype families (Ia, Ib, Id, Ie and If). Cryptosporidium parvum was found in 20% of the isolates, and three subtype families were identified (IIc, IIe and IIb), with subtype family IIc being the most common. One specimen was identified as C. meleagridis of the subtype family IIId. These results are in accordance with findings from other developing countries and report for the first time the presence in South Africa of C. meleagridis, various subtypes of C. parvum and the subtype family Ie of C. hominis. The results suggest that C. hominis and anthroponotic C. parvum subtypes are the major cause of cryptosporidiosis in South Africa. Further molecular studies are needed to better understand the epidemiology and public health importance of Cryptosporidium in humans in South Africa.

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.

rica 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.

Summary This report describes bilateral mammary gland infection with a previously unidentified Cephalobus species of nematode. Only one previous case of verminous mastitis due to a Cephalobus species has been reported, pre‐dating the widespread use of molecular diagnostics. This report describes the case presentation and management, as well as the morphological and molecular methods of nematode identification.