Ten simple rules for the sharing of bacterial genotype-Phenotype data on antimicrobial resistance.

The increasing availability of high-throughput sequencing (frequently termed next-generation sequencing (NGS)) data has created opportunities to gain deeper insights into the mechanisms of a number of diseases and is already impacting many areas of medicine and public health. The area of infectious diseases stands somewhat apart from other human diseases insofar as the relevant genomic data comes from the microbes rather than their human hosts. A particular concern about the threat of antimicrobial resistance (AMR) has driven the collection and reporting of large-scale datasets containing information from microbial genomes together with antimicrobial susceptibility test (AST) results.

Routine use of Xpert® MTB/RIF in areas with different prevalences of HIV and drug-resistant tuberculosis.

Setting: Despite the widespread introduction of Xpert(®) MTB/RIF in developing countries, reports of its use and value in routine conditions remain limited.

Objective: To describe Xpert results in relation to microscopy, treatment initiation, cost and workload under routine conditions at four sites in Cambodia, Georgia, Kenya and Swaziland.

Design: Laboratory and clinical information on presumed TB patients were obtained from routine registers over a period of at least 6 months between March and November 2012.