Mamadou Kaba

A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples.

Differences in the composition of the gut microbiota have been associated with a range of diseases using culture-independent methods. Reliable extraction of nucleic acid is a key step in identifying the composition of the faecal microbiota. Five widely used commercial deoxyribonucleic acid (DNA) extraction kits (QIAsymphony® Virus/Bacteria Midi Kit (kit QS), ZR Fecal DNA MiniPrep™ (kit Z), QIAamp® DNA Stool Mini Kit (kit QA), Ultraclean® Fecal DNA Isolation Kit (kit U) and PowerSoil® DNA Isolation Kit (kit P)) were evaluated, using human faecal samples. Yield, purity and integrity of total genomic DNA were compared spectrophotometrically and using gel electrophoresis. Three bacteria, commonly found in human faeces were quantified using real time polymerase chain reaction (qPCR) and total bacterial diversity was studied using denaturing gradient gel electrophoresis (DGGE) as well as terminal restriction fragment length polymorphism (T-RFLP). The measurements of DNA yield and purity exhibited variations between the five kits tested in this study. Automated kit QS exhibited the best quality and highest quantity of DNA. All kits were shown to be reproducible with CV values ≤ 0.46 for DNA extraction. qPCR results showed that all kits were uniformly efficient for extracting DNA from the selected target bacteria. DGGE and T-RFLP produced the highest diversity scores for DNA extracted using kit Z (H′ = 2.30 and 1.27) and kit QS (H′ = 2.16 and 0.94), which also extracted the highest DNA yields compared to the other kits assessed.

Molecular epidemiology of Methicillin-resistant Staphylococcus aureus in Africa: a systematic review

Methicillin-resistant Staphylococcus aureus (MRSA) infections are a serious global problem, with considerable impact on patients and substantial health care costs. This systematic review provides an overview on the clonal diversity of MRSA, as well as the prevalence of Panton-Valentine leukocidin (PVL)-positive MRSA in Africa. A search on the molecular characterization of MRSA in Africa was conducted by two authors using predefined terms. We screened for articles published in English and French through to October 2014 from five electronic databases. A total of 57 eligible studies were identified. Thirty-four reports from 15 countries provided adequate genotyping data. CC5 is the predominant clonal complex in the healthcare setting in Africa. The hospital-associated MRSA ST239/ST241-III [3A] was identified in nine African countries. This clone was also described with SCCmec type IV [2B] in Algeria and Nigeria, and type V [5C] in Niger. In Africa, the European ST80-IV [2B] clone was limited to Algeria, Egypt and Tunisia. The clonal types ST22-IV [2B], ST36-II [2A], and ST612-IV [2B] were only reported in South Africa. No clear distinctions were observed between MRSA responsible for hospital and community infections. The community clones ST8-IV [2B] and ST88-IV [2B] were reported both in the hospital and community settings in Angola, Cameroon, Gabon, Ghana, Madagascar, Nigeria, and São Tomé and Príncipe. The proportion of PVL-positive MRSA carriage and/or infections ranged from 0.3 to 100% in humans. A number of pandemic clones were identified in Africa. Moreover, some MRSA clones are limited to specific countries or regions. We strongly advocate for more surveillance studies on MRSA in Africa.

The spread of carbapenemase-producing bacteria in Africa: a systematic review

BACKGROUND Carbapenems are the last line of defence against ever more prevalent MDR Gram-negative bacteria, but their efficacy is threatened worldwide by bacteria that produce carbapenemase enzymes. The epidemiology of bacteria producing carbapenemases has been described in considerable detail in Europe, North America and Asia; however, little is known about their spread and clinical relevance in Africa. METHODS We systematically searched in PubMed, EBSCOhost, Web of Science, Scopus, Elsevier Masson Consulte and African Journals Online, international conference proceedings, published theses and dissertations for studies reporting on carbapenemase-producing bacteria in Africa. We included articles published in English or French up to 28 February 2014. We calculated the prevalence of carbapenemase producers only including studies where the total number of isolates tested was at least 30. RESULTS Eighty-three studies were included and analysed. Most studies were conducted in North Africa (74%, 61/83), followed by Southern Africa (12%, 10/83), especially South Africa (90%, 9/10), West Africa (8%, 7/83) and East Africa (6%, 6/83). Carbapenemase-producing bacteria were isolated from humans, the hospital environment and community environmental water samples, but not from animals. The prevalence of carbapenemase-producing isolates in hospital settings ranged from 2.3% to 67.7% in North Africa and from 9% to 60% in sub-Saharan Africa. CONCLUSIONS Carbapenemase-producing bacteria have been described in many African countries; however, their prevalence is poorly defined and has not been systematically studied. Antibiotic stewardship and surveillance systems, including molecular detection and genotyping of resistant isolates, should be implemented to monitor and reduce the spread of carbapenemase-producing bacteria.

Detection of Streptococcus pneumoniae from Different Types of Nasopharyngeal Swabs in Children

Background A better understanding of the epidemiology of nasopharyngeal carriage of Streptococcus pneumoniae is important to assess the impact of vaccination and the pathogenesis of pneumococcal disease. We compared the recovery of S. pneumoniae from nylon flocked, Dacron and rayon swabs. Methods The recovery of S. pneumoniae from mocked specimens using flocked, Dacron and rayon swabs were compared by culture. The yield from paired nasopharyngeal (NP) samples obtained from healthy children sampled with flocked and Dacron swabs was also determined using culture and lytA-targeted real-time polymerase chain reaction (qPCR). Results Using mock specimen, the percentage recovery of S. pneumoniae ATCC 49619 (serotype 19F) strain from the flocked swabs was 100%, while it was 41% from Dacron swabs and 7% from rayon swabs. Similar results were observed for S. pneumoniae serotypes 1 and 5. S. pneumoniae was cultured from 18 of 42 (43%) paired NP samples from the healthy children (median age 8 [interquartile range (IQR) 5–16] months). The median number of colony-forming units (CFU) recovered from flocked swabs was two-fold higher (8.8×104 CFU/mL [IQR, 2.0×102 – 4.0×105 CFU/mL]) than Dacron swabs (3.7×104 CFU/mL [IQR, 4.0×102–3.2×105 CFU/mL], p = 0.17). Using lytA-targeted qPCR from paired NP samples, the median copy number of S. pneumoniae detected from flocked swabs was significantly higher than from Dacron swabs (3.0×105 genome copies/mL [IQR, 1.3×102−1.8×106] vs. 9.3×104 genome copies/mL [IQR, 7.0×101−1.1×106]; p = 0.005). Conclusion Flocked swabs released more S. pneumoniae compared to both Dacron and rayon swabs from mock specimens. Similarly, higher bacterial loads were detected by qPCR from flocked swabs compared with Dacron swabs from healthy children.

Current Knowledge and Future Research Directions on Fecal Bacterial Patterns and Their Association with Asthma

CITATION: Claassen-Weitz, S., et al. 2016. Current knowledge and future research directions on fecal bacterial patterns and their association with asthma. Frontiers in Microbiology, 7:838, doi:10.3389/fmicb.2016.00838.

Fecal Carriage of Staphylococcus aureus in the Hospital and Community Setting: A Systematic Review

Background and rationale: Staphylococcus aureus fecal carriage has been identified as a potential source for nosocomial transmission and a risk factor for disease development. This systematic review determined the overall S. aureus [including methicillin susceptible and resistant S. aureus (MSSA and MRSA)] fecal carriage rates within the community and healthcare settings. Methodology: Peer-reviewed articles indexed in Medline, Scopus, Academic Search Premier, Africa-Wide Information, CINAHL, and Web of Science were identified using applicable and controlled vocabulary through to 11 November 2015. Eligible studies were ascertained by three independent reviewers. Random-effects meta-analyses of proportions were performed to determine S. aureus, MSSA and MRSA fecal carriage rates reported by eligible studies. Results: Twenty six studies were included in this review. The pooled estimates for S. aureus, MSSA and MRSA fecal carriage were 26% (95% confidence interval (CI): 16.8–36.3%), 86% (95% confidence interval (CI): 65.9–97.9%) and 10% (95% CI: 0.7–27.0%), respectively. Fecal S. aureus carriage rates increased on average from 10 to 65% during the first 8 weeks of life, followed by an average carriage rate of 64% at 6 months and 46% at 1 year of life. Genotyping techniques were employed mainly in studies conducted in developed countries and comprised largely of gel-based techniques. Six studies reported on the role of S. aureus fecal strains in diarrhea (n = 2) and the risk for acquiring infections (n = 4). Eight of the 26 studies included in this review performed antibiotic susceptibility testing of S. aureus fecal isolates. Conclusion: This study provides evidence that screening for S. aureus fecal carriage, at least in populations at high risk, could be an effective measure for the prevention of S. aureus transmission and infection in the healthcare and community setting. More well-structured studies need to be conducted and sequence-based genotyping techniques should be employed for the comparison of isolates on a global scale in both developing and developed countries.

Effects of vaccines in patients with sickle cell disease: a systematic review protocol

Introduction Sickle cell disease (SCD) is an inherited haematological disorder caused by a single point mutation (Glub6Val) that promotes polymerisation of haemoglobin S and sickling of erythrocytes. Inflammation, haemolysis, microvascular obstruction and organ damage characterise the highly variable clinical expression of SCD. People with SCD are at increased risk of severe infections, hence the need for vaccination against common disease-causing organisms in this population. We aim to review the evidence on the efficacy and safety of vaccines in people with SCD. Methods and analysis The present systematic review will examine the current data as indexed in PubMed, CENTRAL, EMBASE and EBSCOHost. We will consult Strategic Advisory Group of Experts practice statements, conference abstracts, reference lists of relevant articles, WHO ICTRP trial registry and experts in the field. Two authors will independently screen search outputs, select studies, extract data and assess risk of bias; resolving discrepancies by discussion and consensus between the two authors or arbitration by a third author when necessary. We will perform a meta-analysis for clinically homogenous studies. Evidence from clinically diverse studies will be aggregated using narrative synthesis of the findings. In either case, we will use the GRADE approach to assess the strength of the available evidence. Ethics and dissemination The study draws on data that are readily available in the public domain, hence no formal ethical review and approval is required. The findings of this review will be disseminated through conference presentations and a publication in a peer-reviewed journal. PROSPERO registration number CRD42018084051.

Erratum to: Urban Health Research in Africa: Themes and Priority Research Questions

Oni is with the Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; Smit and Parnell are with the African Centre for Cities, University of Cape Town, Cape Town, South Africa; Matzopoulos is with the Burden of Disease Research Unit, South African Medical Research Council, Cape Town, South Africa; Hunter-Adams and Alaba are with the Health Economics Unit, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; Pentecost is with the Department of Anthropology, University of Cape Town, Cape Town, South Africa; Pentecost is with the Institute of Social and Cultural Anthropology, University of Oxford, Oxford, UK; Rother is with the Division of Environmental Health and Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; Albertyn is with the Children’s Institute, Department of Paediatrics, University of Cape Town, Cape Town, South Africa; Behroozi is with the Primary Health Care Directorate, University of Cape Town, Cape Town, South Africa; Kaba is with the Division of Health Economics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; Kaba is with the Division of Medical Microbiology, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa; van der Westhuizen is with the Alan J Flisher Centre for Public Mental Health, Department of Psychiatry andMental Health, University of Cape Town, Cape Town, South Africa; Shung-King is with the Division of Health Policy and Systems, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa; Levitt is with the Chronic Disease Initiative for Africa and Division of Diabetic Medicine and Endocrinology, Department of Medicine, University of Cape Town, Cape Town, South Africa; Lambert is with the Division of Exercise Science and Sports Medicine, Department of Human Biology, University of Cape Town, Cape Town, South Africa. Correspondence: Tolu Oni, Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa. (E-mail: tolullah.oni@uct.ac.za) The online version of the original article can be found at doi:10.1007/s11524-016-0050-0.