To determine the epidemiology of Candida auris in South Africa, we reviewed data from public- and private-sector diagnostic laboratories that reported confirmed and probable cases of invasive disease ...and colonization for October 2012-November 2016. We defined a case as a first isolation of C. auris from any specimen from a person of any age admitted to any healthcare facility in South Africa. We defined probable cases as cases where the diagnostic laboratory had used a nonconfirmatory biochemical identification method and C. haemulonii was cultured. We analyzed 1,692 cases; 93% were from private-sector healthcare facilities, and 92% of cases from known locations were from Gauteng Province. Of cases with available data, 29% were invasive infections. The number of cases increased from 18 (October 2012-November 2013) to 861 (October 2015-November 2016). Our results show a large increase in C. auris cases during the study period, centered on private hospitals in Gauteng Province.
We examined fecal specimens of patients with diarrhea from 3 continents for Tropheryma whipplei and enteropathogens. T. whipplei was most common in South Africa, followed by Singapore and Germany. ...Its presence was associated with the presence of other pathogens. An independent causative role in diarrhea appears unlikely.
Parvovirus B19 comprises three distinct genotypes (1, 2, and 3). The distribution of B19 genotypes has not before been examined in South Africa. Two hundred thirty-nine laboratory samples submitted ...to a diagnostic virology laboratory for parvovirus DNA detection were analyzed retrospectively. Of the 53 PCR-positive samples investigated, 40 (75.4%) were identified as genotype 1 by genotype-specific PCR or consensus NS1 PCR and sequencing and 3 (5.7%) as genotype 2 and 10 (18.9%) as genotype 3 by analysis of NS1 sequences. Furthermore, phylogenetic analysis identified two genotype 1 sequences which were distinct from the previously described genotypes 1A and 1B. Interestingly, a genotype 2 virus was detected in the serum of an 11-year-old child, providing evidence for its recent circulation. This is the first study to demonstrate the concurrent circulation of all three genotypes of B19 in South Africa and the provisional identification of a novel subtype of genotype 1. The implications of parvovirus B19 variation are discussed.
Background: Candida auris is an emerging multidrug-resistant fungal pathogen associated with high mortality. Methods: We investigated the genetic relatedness of clinical C. auris isolates from ...patients admitted to either public- or private-sector hospitals, which were submitted to a reference laboratory from 2012 to 2015. Patient demographics and clinical details were recorded. We performed antifungal susceptibility testing, sequencing of the hotspot 1 and 2 regions of the FKS1 and FKS2 genes for all isolates with an echinocandin minimum inhibitory concentration (MIC) of ≥1 μg/mL and cluster analysis using multilocus sequence typing.Results: Eighty-five isolates were confirmed as C. auris. The median patient age was 59 years inter-quartile range (IQR): 48–68 years, with male patients accounting for 68% of cases. Specimen types included urine (29%), blood (27%), central venous catheter tips (25%), irrigation fluid (7%), tissue (5%), respiratory tract specimens (4%) and other (3%). Ninety-seven per cent of isolates were resistant to fluconazole, 7% were resistant to both fluconazole and voriconazole, 8% were resistant to both fluconazole and echinocandins (considered multidrug resistant) and all were susceptible to amphotericin B. Of the 15 randomly selected fluconazole-resistant isolates, 14 isolates had an isavuconazole MIC ≤ 1 μg/mL. No FKS mutations were detected. Multilocus sequence typing (MLST) analysis grouped isolates into two clusters: cluster 1 and cluster 2 comprising 83 and 2 isolates, respectively.Conclusions: Azole-resistant C. auris strains circulating in South African hospitals were related by MLST, but the possibility of nosocomial transmission should be explored using a more discriminatory technique, for example, whole genome sequencing.
Objective. To assess the value of routine polymerase chain reaction (PCR) analysis on intraocular fluid from patients presenting with a first episode of suspected active infectious posterior uveitis ...in a population with a high prevalence of human immunodeficiency virus infection. Design. Retrospective, interventional case series. Participants. 159 consecutive patients presenting at a tertiary care hospital over a five-year period. Methods. PCR analysis was performed for cytomegalovirus, varicella zoster virus, herpes simplex virus types 1 and 2, Toxoplasma gondii, and Mycobacterium tuberculosis. Results. PCR analysis confirmed the initial clinical diagnosis in 55 patients (35%) and altered the initial clinical diagnosis in 36 patients (23%). The clinical diagnosis prior to PCR testing was nonspecific (uncertain) in 51 patients (32%), with PCR providing a definitive final diagnosis in 20 of these patients (39%); necrotizing herpetic retinopathy and ocular toxoplasmosis were particularly difficult to diagnose correctly without the use of PCR analysis. Conclusion. The clinical phenotype alone was unreliable in diagnosing the underlying infectious cause in a quarter of patients in this study. Since the outcome of incorrectly treated infective uveitis can be blinding, PCR analysis of ocular fluids is recommended early in the disease even in resource poor settings.
Pneumocystis pneumonia (PCP) is a major cause of hospitalization and mortality in HIV-infected African children. Microbiologic diagnosis relies predominantly on silver or immunofluorescent staining ...of a lower respiratory tract (LRT) specimens which are difficult to obtain in children. Diagnosis on upper respiratory tract (URT) specimens using PCR has been reported useful in adults, but data in children are limited. The main objectives of the study was (1) to compare the diagnostic yield of PCR with immunofluorescence (IF) and (2) to investigate the usefulness of upper compared to lower respiratory tract samples for diagnosing PCP in children.
Children hospitalised at an academic hospital with suspected PCP were prospectively enrolled. An upper respiratory sample (nasopharyngeal aspirate, NPA) and a lower respiratory sample (induced sputum, IS or bronchoalveolar lavage, BAL) were submitted for real-time PCR and direct IF for the detection of Pneumocystis jirovecii. A control group of children with viral lower respiratory tract infections were investigated with PCR for PCP.
202 children (median age 3.3 inter-quartile range, IQR 2.2 - 4.6 months) were enrolled. The overall detection rate by PCR was higher than by IF 180/349 (52%) vs. 26/349 (7%) respectively; p < 0.0001. PCR detected more infections compared to IF in lower respiratory tract samples 93/166 (56%) vs. 22/166 (13%); p < 0.0001 and in NPAs 87/183 (48%) vs. 4/183 (2%); p < 0.0001. Detection rates by PCR on upper (87/183; 48%) compared with lower respiratory tract samples (93/166; 56%) were similar (OR, 0.71; 95% CI, 0.46 - 1.11). Only 2/30 (6.6%) controls were PCR positive.
Real-time PCR is more sensitive than IF for the detection of P. jirovecii in children with PCP. NPA samples may be used for diagnostic purposes when PCR is utilised. Wider implementation of PCR on NPA samples is warranted for diagnosing PCP in children.
This article presents a case of an HIV-infected paediatric patient with an unusual Mycobacterium genavense infection with predominantly abdominal organ involvement.
Abstract Background The presence of Epstein-Barr virus (EBV) DNA in cerebrospinal fluid (CSF) is used as a marker of HIV-associated primary central nervous system lymphoma (PCNSL). In our setting, ...EBV DNA is frequently detected in the CSF of HIV-infected patients with miscellaneous neurological diseases and thus its presence is a poor predictor of PCNSL. Objectives To determine whether quantification of EBV DNA in CSF improves its diagnostic specificity for PCNSL. Study design EBV viral loads were determined on CSF samples from 55 HIV-infected patients with CNS disease. Results Twenty of the 55 patients had detectable EBV DNA in their CSF (median viral load 6120 copies/ml, range 336–1,034,000 copies/ml). PCNSL was confirmed in 2 patients. Their CSF EBV loads were 1,034,000 and 15,460 copies/ml, respectively. Using a cut-off of 10,000 copies/ml improved the specificity and positive predictive value (PPV) compared to a qualitative result for the diagnosis of PCNSL (96% vs. 66% and 50% vs. 10%, respectively). Conclusion EBV DNA is commonly detected in CSF of HIV-infected patients. Quantitative PCR improves the diagnostic specificity, however, the PPV remains too low for it to be used as an isolated marker for PCNSL.
PDF
