Graphical abstract

No abstract

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network.  It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented.  For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations.  We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent.  We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines.  Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

Background. Despite the recent advancement in diagnostic methods, the smear microscopy remains the gold standard for the diagnosis of pulmonary tuberculosis in high burden countries like Ghana. Notwithstanding, fluorescence staining technique provides a more efficient option for the detection of Mycobacterium tuberculosis positive smears. This study therefore aimed at assessing the diagnostic performance of fluorescence microscopy (FM) and Ziehl-Neelsen (ZN) staining techniques in the diagnosis of pulmonary tuberculosis. Methods. A comparative study was carried out on 100 patients who reported at the Out Patients Department (OPD) or the Directly Observed Therapy (DOT) center of the Kade Government Hospital and were suspected of having pulmonary tuberculosis. Two (2) sputum samples each were collected. This included one spot and one morning sample. The smears were prepared and stained with FM and ZN staining techniques. Xpert MTB/RIF assay was also performed. Results. Of the 200 samples analyzed, 71 (35.5%), 46 (23.0%), and 84 (42.0%) were positive for pulmonary tuberculosis when FM, ZN, and XPERT MTB/RIF assays were used, respectively. The mean reading time of FM was three times faster than the ZN technique with very good acceptance (1.5min: 4.6min). The sensitivity and specificity of fluorescent staining to that of XPERT MTB/RIF assay were 84.5% and 100%, respectively, while those of ZN staining were 54.8% and 100%, respectively. Conclusion. For a routine laboratory test in a resource-limited setting, our study has demonstrated that fluorescence staining technique is a more sensitive test for the diagnosis of pulmonary tuberculosis as compared to the conventional ZN technique.

Accurate census data are important in the design, implementation and interpretation of community studies and intervention trials. We outline the methods by which census data can be collected in rural and semi-urban sub-Saharan African villages, and emphasize the importance of painstaking, thorough work in the collection of such data.